As others have already said, I think social conditioning and the resultant self-hate has a big role to play in this.
When I think about why I've taken so long to understand myself, I believe that the reason is partly biological, i.e. partial but insufficient androgenization of the brain, and partly social, i.e. the generally prevalent transphobia and strict gender norms in society. But if I think about why is it so difficult to accept myself, I think it is all social.
Moreover, the longer one lives in their assigned-at-birth gender, the more likely that relationships, career plans etc add to the difficulty of even thinking about transitioning or of accepting one's true gender identity. So we all tend to push it away inside us until it can no longer be contained.
Another thing is that even if one transitions, so many of us still want to align ourselves with one of the binary genders, that I think it reinforces the existing norms in some way. So for those who do not identify with the binary genders or who are uncertain about how transition will pan out for them, it may be even more difficult.
For example, in my own case, I know that I can continue to be fully accepted by everyone as male if I continue living this way, even if I find it hard to imagine being happy or living too long like this. There is a much smaller chance that I can successfully transition and be accepted as female, and still have a good life. It is a small chance but it exists.
But if my transition goes awry, if I am not fully accepted as either male or female, then I see almost no chance of acceptance from anyone around me, not even the people closest to me, and no hope of a career or a good life of any sort.
All of these thoughts just add up and still make it difficult for me to fully accept myself, even if I see no other way of describing my gender identity except female.