I recently traveled on Amtrak in the Northeast corridor dressed 'in between', and no one batted an eye or said anything.
I was wearing this sweater (http://www.landsend.com/products/wom...uery=447394OHX) with a VS 'add two cups' bras underneath (which are very molded so you definitely saw significant bumps under the sweater) and a tight waist cincher that made the sweater look right. I had women's skinny jeans on, and women's flats.
No makeup or wig, though I do have shoulder length hair. But I have a 5 o'clock shadow by 9 am if I shave at 7, so there is no mistaking my real gender unless the lighting is poor and the makeup is heavy.
There are morons and assholes, of course, but most people are good people, and don't care what you are wearing as long as you aren't a jerk to them, I think.