I had doubts all throughout transition.
But the real thing is, I realized that my doubts were all based on fear... fear of others judging me, fear of acceptance, fear of being rejected by women and seen as a freak and an invader of their spaces, fear of how embarrassing it would be to go before people I knew as a guy but now with a female body, (my dad especially,) and just something about the binary label of "woman" and all of the social connotations that came with it didn't quite click with actually seeing myself as one, even though I was still constantly jealous of them. Plus, as others have mentioned, a fear that I would change my mind and have to go back.
What kept me going was realizing that all of these fears were all completely based on other people's reactions, and all based on cultural binary notions of femininity. When I thought about it at an absolute level, there was no doubt in my mind that I wanted to see a girl in the mirror, I wanted smooth skin, I wanted SRS, I wanted long hair, I wanted boobs, I wanted to wear female clothes, and I wanted to be a girl physically in every single way. I realized that in a vacuum or on a deserted island or something, where I was completely by myself and never had to interact with anyone else, and I would never have to worry about a single person judging me or even looking at me, I would transition in an instant with no doubts whatsoever. The only thing that was holding me back was fear of other people's reactions and acceptance, and fear of being a trans woman in society at large.
I guess a big thing was that every single time I had a dream where I was a girl, it was one of the happiest dreams I'd ever had. I'd look at myself and feel like my heart was leaping out of my chest because I was so happy. Where dreams of masculinizing further, such as going bald or looking in the mirror and seeing a middle-aged guy looking back at me, were always complete and total nightmares. (The only bad "girl" dream I ever had was one where I turned into a girl and I was naked and I had people staring at me and laughing.

)
So while all of my fears were indeed genuine fears, which are still causing me problems, they are a reflection of society's attitude toward trans people, and gender in general, not genuine doubts about my gender identity. In regards to that, my premonition was correct. And now I'm at the point where, for the first time in my entire life, I'm actually starting to like my appearance and be happy with who I am.
I think that's the key. Just explore your motivations, explore your fears, and figure out whether they're coming from social pressure, or what you yourself would want if not a single other person was involved.