Can Theists Get Out of It?

And, no, I'm not referring to substance abuse (this time). I'm talking here about the penchant I see amongst theists to state, "Oh, we're different than other denominations" or, "I speak as an individual and don't necessarily go with what our Church says"....... in particular, when it comes to the bigotry and prejudices that Churches are notorious for inciting and harboring.

Specifically, (like that word, Elpers?) specifically here, I am raising the issue of "guilt by association". And, hey, I know the "G" word does tend to lift the hairs on the backs of most theists, but we are dealing with a pertinent societal (like the au moderne adjective there?) issue so it's worth unpacking it and peeling back the layers to see where the onion skins fall.

For example, as we all (should) know, the Ku Klux Klan is an American white supremacist terrorist hate group well known for its (yes Maxx, "its") ugly bigotry towards minority groups. If you were to see me walking down your local high street wearing a white, hooded gown and carrying a burning cross, it would be reasonable for you to label me as being a hateful, ignorant, arrogant bigot. If I were then to counter with the (lame) argument of, "Oh look, I'm not like the rest of them and I don't agree with their policies, I'm just a member because I like the comradery and the beer is cheap and, oh, is that the time?.....he, he", it won't exactly make the cut in the credibility stakes, would it?

So, given that, for example most Churches, especially the Catholic Churches are homophobic (yes, they are) and, given that you are a member of one of said institutions, would it not be fair and reasonable for you to be labelled as being homophobic and, or bigoted? 
In other words, would you not be "guilty by association"?