Why did the church make it hard for Leonardo Da Vinci?

Answer 1

Church had all the money, if you were a craftsman like Leonardo you had to depend on someone to fund your visions and creativity. Thus Leonardo designed weapons of war, but I digress. The church like any patron required that the artist's vision coincide with the patrons or the funding is revoked.
This was a constant source of conflict.

Answer 2

Maybe because he was homosexual.