I have the same problem liking James and Sirius in HP as I have liking Antonio and Bassanio. And I have the same conflicted desire to redeem Snape as I have with Shylock.
Telling me that characters are the good guys does NOT tend to make me favorably disposed towards them; it tends to make me skeptical and suspicious about what sorts of social compromises they were involved in to put them in that position, whether they got lucky by birth or temperament or the way they chose to fit in. I don't tend to NOT like characters because they're the heroes (I love both Aubrey and Maturin in Master and Commander even though they are clearly and indubitably the good guys and the deck is stacked in their favor in so many ways) but it doesn't make me an automatic fan.
And in the case of James in particular, as I said, I feel like I'm being shown a golden boy, with a good family both in terms of breeding and temperament, with talents that other people won't equal with any amount of work because he's just got the gifts, and he acts like a bastard out of BOREDOM. That reminds me of The Merchant of Venice, and Snape, like Shylock, is really HARD to like -- you have to believe that there is so much more to him than you're seeing from the prejudiced protagonists' point of view. It's impossible, with Shylock, for me really, because to root for him is to root for a patriarchal system that oppresses his own daughter, where someone like Portia is not possible...and yet her "mercy" is like Lily's mercy, the thing that's possible for her because she's already popular. I don't like the "villain" and yet I despise the heroes, for they have made him the outcast, the scapegoat, and if he threatens their way of life, it is only because of what they've made him become.
I am not trying to draw really substantial parallels here, but I was thinking about the play and it suddenly hit me that my emotional reaction to the Marauders has some distinct parallels. Lupin's as much a victim as Snape in many ways, so I excuse him, and Sirius has an awful lot of darkness back home. But James? No, I don't care what label is put on him, he will never be a hero to me.