Yes unfortunate to say but Phoebe and Cole were toxic for another and should never have been together.
I can see and understand why some (not all) feel like it's a "toxic" relationship. I (also) believe they compliment each other, really well, as they both share the same and/or similar personality. They're both survivors and can do questionable things.
Even before Phoebe met Cole (and even S3E17 "Pre-witched" shows this, as well), Phoebe is known to be a little trouble-maker (even mentioned in S6E17 "Hyde School Reunion), herself, but she does has her own standards in what she feels is the right thing to do (similar to Cole, which I'll go over, in a minute). That's why it's shown for her character (specifically) to be shown doing the murdering in the S2E2 "Morality Bites" future (IMO) and not Prue nor Piper. Time and time again, we see hints of Phoebe's character (or general representations of her character like P. Russell in S2E14 "Pardon My Past") doing questionable things/having a dark side to her, so it's only natural and/or logical for her to fall in love with somebody who understands this mentality. And why both her and Cole compliment each other. I even think the Seer knew how much Phoebe craved power but disguised it under the form of a lie, that Phoebe later uses as her own personal excuse, but I digress.
The reason I feel like Cole has his own standards in doing what he thinks is right, is what he did in S3E4 "All Halliwell's Eve". What was Cole doing that caused him to shimmer from nowhere, to the Grimlocks harming a child, that was nowhere near him? He even questions them and even commands them to stop harming a child. This very scene shows a much more nuanced character depth than just a black and white morality concept, similar to Phoebe's character. Later on, in S3E5 "Sight Unseen", the Triad were growing impatient with Cole's attempts in killing the Charmed Ones, and Cole blurts out (very quickly) how angry he is 'cause this was a job for him to obtain something (it was never clear, in this episode, at least). So, killing the Charmed Ones wasn't an idea that popped into his head to do. He was assigned / ordered to do so, as a deal with the Triad and to be rewarded with something. I like to think that reward was his father's soul (as mentioned in S3E20 "Exit Strategy", but I digress). So, this wasn't something he wanted to do, but what he was ordered/instructed to do. As far as he's concerned, he doesn't give a flip if the Charmed Ones are alive nor dead, on a personal level. They're not a threat to him, as Cole (kinda) admits to dealing with Vampires, in S4E18 "Bite Me" even though they were exiled by the original Source. Which leads me to believe that the original source was no threat to him, either, if he's comfortable enough to be working with an exiled species, of the underworld.
So, both Phoebe & Cole are a bit more than simply just "black & white". Which made them so interesting (to me) because of how "morally gray" they were. OFC, we all know that Phoebe does change and after going through a particular life experience, in my life, I can (now) relate to Phoebe's decision in no longer wanting to associate herself with Cole and black magic because of how addicted she was to the craving, desire, enticement, etc., of it all. So, she basically decided to cold turkey it all away. I began noticing I really only dislike Phoebe in S5a. Otherwise, I'm fine with her in S5b-S8. But, I (also) understand why Phoebe did what she did in S5a. And, I still wished that Cole never found a way out of the Wasteland, at the end of S4E22 "Witch Way, Now?". It really ruined his character, and the romantic tragedy that was Phoebe & Cole, but I digress.
With Phoebe having been born in the manor the same as Wyatt and with the Shadow under the basement she and he were more susceptible to evil as illustrated by the Woogy even though that could've possessed Piper or Prue instead of course.
There is this, as well.
This could partly explain also why Phoebe chose to be Queen Of The Underworld but then some might argue Paige's point in the episode with the Manticore baby that folks aren't predisposed to evil but have to want to be that themselves overall.
Which goes back to my point regarding how I feel open into calling Source Cole's situation as a "decision", as long as we acknowledge that Woogy Phoebe's situation is the same. Considering, the dialogue expressed in both S1E15 "Is There a Woogy, in the House?" and S1E18 "When Bad Warlocks Go Good".
Dialogue said in S1E15 "Is There a Woogy, in the House?"
Dialogue said in S1E18 "When Bad Warlocks Go Good". I'll (also) be adding something else Prue said, that caught my attention, as well, but I digress.
What I find fascinating about the last line said in the S1E15 "Is There a Woogy, in the House?" dialogue is the line (despite being in an altered voice) stating that Phoebe is now stronger than Prue but said through the Phoebe perspective via "No I wasn't. That's why he chose me." Later then to say because of the shadow/Woogy Phoebe is now superior to Prue? Interesting choice of words.
And, Prue's dialogue in both S1E15 "Is There a Woogy, in the House?" and S1E18 "When Bad Warlocks Go Good" talking about even if it may look like something has taken over, doesn't mean it's 100%, and there's still a struggle happening, within. Even though, Woogy Phoebe froze, the fact that Prue says that the shadow hadn't completely taken over otherwise both Piper & Prue would be dead...reminds me of Source Cole's position in ensuring the safety of Phoebe. Because Phoebe loves her sisters and doesn't want anything to happen to them, she fought for their safety, and the same goes for Cole. The Source might've tried to take over Cole but couldn't completely do it, as Cole's love for Phoebe is too strong, for that to happen.
And, Prue's comment regarding the struggle, is an exact replica of what was going on with Cole. I (also) found Prue's commentary interesting in reminding everyone (and the writers reminding the audience) that Brendan is not just a warlock, he's human too. Which is what Cole is, as well. Which is why I find it very frustrating, when later on, in S3 Prue tells Cole he'll always be evil because he's a demon while completely disregarding his human side but gives excuses to Brendan, but I digress.
So, I'm open to the idea of it being a choice, as long as we acknowledge that it was the same for (specifically) Woogy Phoebe because I can't find any real logical explanations for Wendigo Piper. Wendigo Piper felt more genuine in a Wendigo taking over. Whereas, Woogy Phoebe felt way more nuanced and complex for it to be really clear especially, when we look at the dialogue.
All I know is that in Charmed In Dangerous Cole wanted to save Phoebe and then in turn her sisters and that the only way to do it at the time was to absorb the Hollow so he could strip the Source's powers before they were returned which the Seer told him would happen so he believed her no doubt.
Of course, we all know that was a lie afterward but at the time he didn't so one might say what happened subsequent wasn't his fault but then I've read comments where fans have queried why Cole didn't know about the Hollow's powers or that the Seer lied having been a former demon himself so what did happen was his fault but then I tend to lean slightly more towards the first point and not the second one myself.
Agree.
EDIT: The only logical explanation I can come up with (regarding Wendigo Piper) is Wendigo Piper following the lead of the main Wendigo's desire. But since Wendigo Piper froze the flare gun bullet and ended up freezing the real Wendigo, Wendigo Piper looked rather confused and kept looking back and forth between her sisters and the main Wendigo. I'll even mention Wendigo Piper didn't freeze, then again Piper is the main source of said power, so...why would it freeze Wendigo Piper? xD