You're not imagining the Alec animosity, but I will say that it's nothing compared to the Logan/Michael Weatherly hate I've seen in other areas of fandom. And I think that's my biggest issue with the whole Alec thing. I actually like the character, but I can't stand the way the Alec/JAckles fans act like he's the only worthwhile part of this show. "It should have been Dark Alec", "Logan should have kicked the bucket," blah blah, woof woof.
I really, really enjoy the camaraderie that develops between him and Max. It strikes me much more as a sibling-ish "you're family, but I still want to kill you most of the time" vibe rather than a romantic thing. And honestly, if a Max/Alec pairing were to happen, I think a lot of the things I like about the character would be gone. What's funny is that he's supposed to be this big "obstacle" to M/L, or that's how some of the M/L shippers see it, but on the show, most of the time he's encouraging Max and Logan to get on with it. Mockingly, yes, but it comes from a good place, I like to think. He respects Logan, and he cares about Max, and I just don't see anything developing to change that.
So basically, once again it's the fans causing trouble where there really shouldn't be any. In my opinion. *shrugs*
And lastly, the early S2 hair + the godawful glasses aren't doing my beloved Logan any favors. I think I may have cheered a little bit when he got his hair cut.