Most vegetarians on Earth abstain from meat because of the treatment of animals as a result of mass proceessing. However in a universe with replicators, there is no ill treatment. A replicator simply aligns the molecules in such a way as to create a version of the food.
No animals were harmed in the replication of this cheese burger.
The proliferation of replicator technology has probably made the use of real livestock all but extinct. Additionally given the nutritional advantage of meats being a complete protein, it doesn't seem logical to arbitrarily deny that source of food.
Why are Vulcans (or anyone) vegetarians in the Star Trek universe?