Hmmm, not since they banned speaking openly about homosexuality have I seen a thread so infested with judgemental, narrow-minded people. Reading these pages has given me a sad and about half drained my daily serving of faith in humanity, so kudos on that I suppose.
As to the the OP....
The thing is, Justagirl, some people are so used to putting everyone they see in one of two boxes that when they encounter someone who doesn't really fit in either box, it makes them very uncomfortable. They've forgotten that there's more than two boxes, that there are as many boxes as there are people.
You're probably going to run into that a lot and I'm sure you don't need me to tell you that. The reason this kind of box thinking seems more concentrated around church is probably because that's where a lot of the box thinking is learned from in the first place. They are taught that god made Adam and Eve, not Adam and Eve and Leslie-the-not-totally-like-Adam-or-Eve. And probably having you there, looking like a girl, sounding like a girl, being called by a boy's pronouns, having male parts, is a reminder of that. A reminder that not everything in the world is explained by their book and their boxes. It probably scares them silly, and that's why they take it out on you, want you to conform to something you're not, want you to choose a box and stay in it, even if it means doing unnatural things to your body just to fit better. They'll tell you that you're sinful, that you're being disruptive, that you have to dress a certain way or you're not allowed in their little club. Don't listen to them. Sounds like you already aren't, which is great.
Wear skirts if you're into them. (Something most guys will never know--skirts are super comfy.) And date girls if you're into them too. A lot of girls are going to see definite advantages to having a boy/girlfriend. Being a blend of genders gives you the chance to be the best of both. Go ahead and be somewhere in between, it won't matter to the people who matter. As a totally straight woman, people assume I'm a lesbian all the time, just because my best friend has short dyed hair and we go everywhere together. The key is not caring and finding other people who won't either.
On that front, it's obvious that your religion is pretty important to you. This may sound like odd advice from a heathen atheist like myself, but you should never let a bunch of idiots stop you from participating in something that is important or meaningful to you. If you liked that church, keep going to it, and keep wearing what makes you comfortable. What are they going to do, bar the doors? Eventually they might even be able to overcome their prejudices and stop popping their monocles when you walk through the door.
But you asked 'why can't they focus on religion instead of societal structures?' And the answer is that church is far more about social structure than religion and always has been. After all, Jesus himself condemned public displays of piety and said it was better to go into an empty room and be spiritual alone with your god. So why all the big freaking buildings with bells in them? Because people get bored in an empty room by themselves with god.
You should look for the social structure that's right for you. So if you don't feel like going back to your old church, and I wouldn't blame you, you should definitely try out some other congregations on your own. I would suggest Universal Unitarians if there is a church in your area. A friend of mine in high school made a project out of spending a sunday at every church in our town and eventually settled on the UU congregation as being the most welcoming, tolerant, and friendly of the lot. Looking back on the few times I went myself, I don't think anyone in the room would have batted an eyelid at your skirt and make-up. Of course, congregations are going to differ widely even within the same branch of a religion, so your experience may not be the same, but I would start there.
Good luck, and don't let the haters bring you down.
