It's due to the fact that fandoms are made up of humans, and that's what humans do. And if you want to engage in any kind of interaction with others or activity, you will get hit with stuff your not going to like. You don't have to change your convictions one bit, but you do have to be prepared to deal with such matters.
Example: the famous voice actor Vic Mignogna has been in countless anime series but has a number of convictions about things that he won't budge on. So if he is doing a signing at a convention, there are some types of artwork he won't sign, and he will ask if they have something else he can sign. So while being exceedingly polite, he maintains his convictions but engages the anime fandom on his terms. So you may have to figure out how to do something in a similar spirit if you are wanting to get involved in MLP fan works.
I hope I'm not be too vague, and that that helps you get a bit of perspective on how to respond in your situation.