Way I look at it is this: there are absolutely things in Islamic theology that are objectionable, specifically concerning homosexuality.
Those are often the very same things that are objectionable in Jewish and Christian theology as well, and come from a similar source: that all these religions arose within cultural contexts in which homosexuality was considered impermissible (and a whole lot of things we today find objectionable were considered permissible - such as slavery). All three, in other words, internalized and were a product of their cultural context.
On the other hand, all three contain attempts to reach beyond the cultural context of their day, to critique aspects of existing culture on the basis of moral values. They were, if you like, a mixture of attempts to reach some sort of universal moral truths, combined with a bunch of dross that mirrored existing prejudices.
The difference between a fundamentalist and a non-fundamentalist is that a non-fundamentalist, whether they know it or not, is always seeking to distil from their religious background (or non-religious moral background, if they happen not adhere to a religious tradition) the gold of moral truths from the dross of background of existing prejudices. You see this process again and again.
A fundamentalist, on the other hand, absolutely refuses to make such discriminations - they are likely to cling to every crumb of dross, all the moreso if others are questioning the validity of a particular crumb. They are likely to take the position that the dross is among the absolute essential parts of the religion or moral philosophy - so to discard it, is to discard the religion (or philosophy).
Now, no religion has a monopoly on fundamentalism. In some no doubt it is more prevalent than in others, due to all sorts of factors. It so happens that right at this moment Islamic fundamentalism is the most problematic variety, and its most obvious manifestation is fundamentalists clinging to the dross of homophobia - probably all the harder, because acceptance of homosexuality is so widespread among those they consider their enemies.
How to deal with this? I’d say, to encourage as much as possible those non-fundamentalists within Islam who are attempting to engage in the process of discarding the dross of homophobia. The worst approach is to assert that the fundamentalists within Islam are, in fact, correct. That is, that somehow homophobia is essential to the religion, and so the only choice is to accept it or to reject Islam.