The replicator is not a straight energy to arbitrary matter machine. It uses a lot of energy to rearrange matter quickly. But there are still storage tanks of basic nutritional components that go into the process. At least that's what the Star Trek Technical Manual says.

Also, the dilithium crystals are allegedly not fuel, but catalysts or moderators. The ships (at least in the TNG era) still fuel up on cryogenic deuterium slush, of which half is converted into anti-deuterium before entering the warp core.

Enterprise-d, at least, had some limited capability to gather fuel from space with the ram scoops. These were the red things on the front of the nacelles.