Morrisson got this and it's evident in the Assault on Weapons Plus arc. Logan can't understand how a guy like Cyke has gotten the women and respect that he has, when Logan thinks he's a pussy. However, at that point Logan finally acknowledges his respect for Summer's abilities, made possible by Logan seeing Scott down and with crippling self doubt of his own.
Post-Morrison, and definitely post Whedon, when Cyke starts to lose the self doubt (maybe he woke up one morning and thought "I lead one of the most powerful para-military forces in the world and bang unimaginably hot girls like its my job... Why do I doubt myself again?) then Logan became resentful of Scott, again, for having something he wanted and could never have.
Almost all of Wolverine's X-Men career has revolved around him wanting what Scott has: Leadership, Jean, respect from his peers for influencing the species (the school), and finally the biggest one: self respect.
Read this way, Logan is not out of character at all. I applaud the writers making him a traitorous dick attempting to murder another of Cyke's grandchildren (Tyler.) I'm just not sure why people don't see this rather layered portrait of a man with crippling self-hatred that projects onto the most successful male around him. (he's sexist too... Where's his hatred of Storm?)