When you use the term 'religion', you are implying that it was the Bible or the Qur'an directly cause homophobia. Well, even if religious texts contain a sense of intolerance for gay people, that doesn't mean religious people are forced to apply them in life. For example. The Bible claimed that masturbation was considered a sin as well as homosexuality. These were not considered moral abominations but rather a deviance from certain norms in society and shouldn't be taken very seriously.
When people talk about some of the things in religious texts that seem ridiculous to us now don't seem to realize that these texts were written thousands of years ago. They were meant for a particular people in a very specific time period. There is nothing absolute in their teachings, and it would be very foolish to think there is anything timeless in them.
There are many religious people out there who accept homosexuals and abortion. So obviously if the statement, 'Religion causes homophobia' were to stand, then all religious people must be homophobic. The problem I think, is in the way people have chosen to interpret and use their religion, but not in religion itself. If I were to tell you that a brilliant scientist created a bomb that he used to kill thousands of people. It would be wrong to say that science is at fault here; it's obvious that the person who chose to abuse science for obscene actions is that one who should be held accountable.