I officially came out to my old high school best friend today... and yeah, same kind of thing. He said "you know, I've never really been comfortable with how society expects men to act either," and I was like "no, no, you don't understand, it's not that, it really is that I identify with the female gender in every way, and hate my male gender in every way... physically, socially, personality-wise, expression, and it's not just how guys are expected to act, it's about actually feeling female, and feeling like everything about who I am gender-wise is wrong." He seemed to kind of get it after a while, and was of course very supportive, but yeah, it's true, it takes a LOT of explaining before cis-gender people really start to "get it," because they really haven't experienced that same sense of wrongness before, just maybe if we're lucky a sense of "I wish guys/girls could do this too, and that society's gender roles weren't so fixed."
The good thing is, lots of people can still be very supportive and very understanding, hell, even happy for us, even if it's hard for them to really understand the pain that we go through. My mom was the same way. She didn't necessarily understand why, but when I described to her how happy I was, and how I finally felt like I was being myself, and felt truly alive for the first time since I was like 12, she was so happy she started crying.
So no, they don't understand all the time. But there are still lots of good people in the world who, even if they don't get it, can still be truly happy for you.