Cyclops killed Professor X in the comics and took over the X-Men at o e point and ran it like a dictator.
Cyclops was possessed by the Phoenix when he did that, a fact that Logan conveniently leaves out when he told a few of his teammates, which when the truth does come out causes a few of them to rejoin Scott's side.
Cyclops was also unfairly made the scapegoat of everything that went down in Avengers vs. X-men (Scott even points out how most of the issues arose from Tony Stark's decisions, which the Avengers have no rebuttal towards. He also points out how the Avengers have rarely stood up for mutantkind specifically even when they needed their help the most, again the Avengers don't have much of a rebuttal). Meanwhile Logan isn't called out for anything afterwards, never mind he casually pushed for the murder of Hope, a teenage girl, to solve their problem when it's the fucking Marvel Universe and they have countless magic/cosmic solutions they could consider before resorting to murdering a minor.
Also in a recent move, mutants were being captured as soon as their powers manifested, so Cyclops tells the "law" to go fuck itself and tries to save as many of these new mutants as his team can.
Now, I only followed the events of what happened with all that for about two years post Avengers vs. x-men, kind of started checking out other books after that plus I wasn't too big on the whole "let's have the original five X-men of the past come to present day" story, so maybe Scott truly does jump off the slippery slope eventually, but a good deal of the stuff post Avengers vs. X-men I was totally siding with Scott.
Especially because, let's be real, if it had been Jean possessed by Phoenix who had killed Xavier, you know Logan would be singing a very different tune. (also let's not act like this wasn't some level of karma for Xavier, not saying he should be killed, but the man has definitely done some morally wrong things up to this point)
Honestly, Logan needs to get over her already. It feels like it's the main thing keeping the rivalry with Cyclops alive which has been long played out, and Jean hasn't been interesting in a long time. Honestly, unless either of them have recently gotten a legit good love interest, I'd love to see him go out with Storm. They've been friends for a long time and I feel they could be good for one another (lord knows it'd be better than Storm dating T'Challa which was so random, the two barely had spoken to each other in the comics before that abruptly became a thing).
And Scott should of course get over Emma as she has messed with him to much in the past for that relationship to ever feel healthy to me. Can't think of anyone he should be dating instead (not Jean either), but it shouldn't be Emma.