I think we must all accept that they are in fact biologically or environmentally flawed to a certain extent, a healthy human is one that has tendencies optimal for procreation and rearing children, with the former at issue though there are plenty of straight people that don't seem to do very well at the latter. That alone does not make it any more acceptible to discriminate against than any other biological flaws, necessarily, as we all have some to a lesser or greater extent.
There is another variable though, the identity of many gay people seems to be in turmoil, most often the younger generation doesn't have enough positive role models and will arbitrarily grasp at someone who is gay merely for being gay, because segments of society can make them feel isolated or estranged. Unfortunately, it is not uncommon for someone who has a stereotypical deviant behavior, to deviate in other ways as well and through association, pass on these limited social mindsets through exposure to someone still developing their own self identity. Take the drama queen for example, it does't seem too far fetched to think a substantially higher % of gays act like this opposed to straight people, but there is no real justification for it from being gay - It is possible that person is emotionally unstable and just happens to be gay too, that a similarly emotionally unstable straight person might reserve their behaviors more in this area.
Some people are just fruit loops. Gay or straight doesn't matter, but to an instable person, the additional stresses of being gay in certain environments could exacerbate their fruitiness. So do other human attributes, but it is only certain minority groups that have tried to declare "we demand to be accepted for who we are" without consideration that being rejected for who they are, may not (always) be because they're gay.
Then there is the paranoia, if a gay person is told to expect prejudice, they will tend to interpret more things as prejudice than had they not expected it. Many things you say to someone are a bit ambiguous to them and could be interpreted a number of different ways depending on the mindset of the listener. This can determine their reaction and subsequent interactions.
In the end, being gay is not necessarily a problem, but it could be a potential problem as could many imperfections. Since there is no perfect human being, any choice on how to react to another person has to be a summary decision, not based on only this one variable, although if there is no sexual context and a person is readily recognized as gay, it is their personality you might take issue with instead of their being gay, so it is a personality discrimination against a gay person, not a gay discrimination against a gay person. This is not meant to justify anti-gay sentiments but on the other hand, seldom are things so black and white as we want to try to make them.
Upon reflection my post seems too critical of gays, but there is a bright side. A gay person today does not have to assume that (being gay) limits them or that it determines how they have to act. Take being an elected official for example, if anyone who had considered running thought to themselves "there's no way I'd be elected", then they may have already concluded the chances of success weren't worth the effort, without ever really knowing. That self-destructive thought pattern can be most problematic of all.