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If he were Islamic he would hold the same views, so are we being "prejudiced" or should we be more tolerant of his position on these subjects ?

This whole "you're fine with Muslims being bigots, but not white people" augment that gets trotted out by the alt right is so basic.

So-called "liberals" don't think being a bigot is fine as long as your brown. They think that you shouldn't make mass (often false) generalisations and pejorative statements about a large group of people. Not all Muslims want to throw gay people off roofs. Lots of them drink, have premarital sex, and all sorts of other things that are prohibited depending on your particular beliefs and how much you think it's necessary to adhere to them... just like Jews or RCs.

... it's almost as if people aren't binary entities who all fall into one of two extremes.

Personally I don't have any issue with JRM holding views informed by his religious beliefs. It's a free country. The point I start objecting is when he uses them to inform his political actions. While it makes sense that his personal informs his political, once you move into the political you're open to criticism. It would be the same whatever denomination he was.

Equally I think it's important to understand that you can have a moral view that runs counter to your opinion on a policy one. For eg, personally I think it's hard to make a sound moral/philosophical case for abortion. However, from a legal and policy perspective I don't think that ranks as a decision factor. Therefore, were I in the position, it wouldn't effect my voting on a bill.

Also the starting point in any discussion is that you should be tolerant of peoples views. You should listen to them, weigh them up on their logic and any evidence available, then form a conclusion.

I've listened to lots of peoples' views on gay marriage and taken them on board. I've yet to hear a convincing one. I'd like to use a cullender analogy, but unfortunately that implies some sort of structure around the holes.