Because it's not a good use of time for one-off modifications. Plus, the GUI is nice for visualizing, so there's a decent chance you're spending a lot of time in there anyway.
It's possible to run a query to modify the contents of a database without changing the schema. You may already be familiar with the UPDATE statement, for instance.
And not every database in existence is part of a larger stack. I don't care much about automating a task I'll only do once in a throwaway DB that exists only on my computer.