Some have posed a theory elsewhere on the forums that many male fans do have a competitive thing going with the male leads, which is clearly what you're getting at. I'm not sure I buy that, but hey, this is the forum where I once saw several posters claiming they would leave their RL guys and/or gals for in game characters, so you never know.
In the case of the four you mention, there's an added complication: Carth. Carth is a bit, well, irritating. Because he and Kaiden have the same voice actor (Raphael Sbarge? I think?), some perceive Kaiden as similar to Carth. Personally, I never saw the similarity based purely on the text; it's just a vocal thing. I actually think Kaiden's quite likeable, although he almost always dies on Virmire in my games because of a different male bias: I have trouble condemning Ash because of her gender, even though I find her kind of unlikeable.
I don't get the anti-Alistair backlash. Sure, he sometimes comes off like that one idiot friend everyone has, and he often appears to lack a spine, but he has redeeming qualities as well and mans up in the end most of the time depending on what the player does.
Jacob: I like this guy. Sometimes he has a "Captian Bland" moment, and his presence in Cerberus is a little puzzling, given that he's a good guy and Cerberus is an organization Miranda unironically describes as "Not AS evil as people think." (ie implying that, yes, they are at least SOMEWHAT evil). Even so, a guy who can face down a suicide mission while declaring his intention to "Get Loud" and "Spill some drinks on the Citadel" is OK as far as I'm concerned.
Gravity is one mean mutha.

I think the root of the issue is that we men have it drilled into our heads from a young age that to be "manly" we have to be in charge. Videogame NPCs, however, are by definition NOT in charge, which complicates the stereotypically "masculine" elements of their personalities. I think this creates a subconscious dislike of these characters in many male fans because the characters somehow don't register as the assertive, masculine men we're socially conditioned to admire. This results in only hardass characters like Wrex and Canderous being "OK" to like because they compensate for not being in charge by not caring about it and kicking lots of ass, thereby dodging the issue.