I wouldn't trust a grammar checker too much, anymore than I'd rely on a spellchecker to find and fix all my mistakes. It's not a bad thing to use either, but a lot of the time it will come back to what you know about writing and what you're trying to do.
That's especially true for fiction writing, which may tend toward being informal or purposefully "wrong" for effect. For a formal writing project, like a business report, it might be a lot more useful.
Now, if I could find something that would read my mind and automatically insert commas for me, that would be really great!