I could start this article a lot of different ways hemming and hawing over the minute technical differences between these two products.  But I won’t.  Instead I’ll just say this:

Which I’ll only temper with “…unless you have no other choice.”

Here are the three big reasons:

1.    There are some minor technical issues, but nothing that the standard small business site with less than a few million record needs to worry about.  MySQL will perform at least as well and often far better than MS SQL server.
2.    MySQL hosting is less expensive.
3.    MySQL databases are easier and less expensive to move.

So why do people ever choose MS SQL server?  It usually has to do with a comfort level with the brand name rather than a technical or financial choice.  If, as a programmer or a computer user you’ve only ever worked with Microsoft products (which is very common), you will naturally move toward what you are familiar with.  As a side note, if your web developer doesn’t know anything about MySQL, the database that has been running the web since its inception, you’ll want to find a new developer.