General Confusion:
* Bewilder
* Disorient
* Mystify
* Perplex
* Puzzle
* Baffle
* Flummox
* Muddle
Misunderstand:
* Misinterpret
* Misapprehend
* Misconstrue
Mix Up:
* Jumble
* Scramble
* Disarrange
Make Uncertain:
* Doubt
* Hesitate
* Ambiguous
Intentional Confusion:
* Deceive
* Mislead
* Trick
The best synonym for "confuse" will depend on the context of the sentence.