MySQL is free, small, easy to set up.
MS-SQL is expensive,big, and more complex to set up.
But MS-SQL has a much more complete SQL language than MySQL.
So if you want a quick and cheap solution, use MySQL (or pg-sql) but if you want complete SQL (and you already have an MS-SQL server handy) use MS-SQL.
Dislaimer: MySQL and pg-sql are fully capable of running huge databases for huge websites, you don't need MS-SQL or Oracle for that.
But... if things go belly-up there's no expert you can call to have a look at it.
Choices choices...