it depends on the story
Evangelion has a fucked up unhappy ending but I've always liked it
and if I feel the story has meritt outside of it's homophobia I'll occasionally overlook anything I find homophobic
heck I kept watching YuYu Hakusho and Hunter X Hunter even though the only gay characters in both were evil and got killed
and frankly had people not told me I should love Puri Puri Prisoner "just because he's gay" I probably could've overlooked him
somehow the fact that people were insisting that I should like him just because I'm gay made me resent the show as a whole
my current strategy is to just flat out deny any anime characters are gay(even the ones that actually are) so I can enjoy the show in spite of how terrible the few canonically gay ones all are and not get my hopes crushed