Simply because when the site was young, we repeatedly had folks posting questions about "query" when they really meant "help me with my sql" and don't understand the esoteric differences of the description of higher order math and the relations of sets.
Maybe you can make some Tag-Wiki suggestions to help people understand the differences, and we can evaluate removing the suggested synonym?
This is no longer the case. The synonym was removed in July 2018:
See Remove [query] as synonym for [sql] for the discussion.