Flatfile is good but be sure you're making a backup!

Last thing you need is the file to get corrupted because it was trying to read and write at the same time. This is where MySQL would be helpful as the table is locked during the write process. Depending on what flatfile system you're using you can lock the database there too.
Years ago, and I mean years, maybe 10, I wrote a CGI troubleticket system for a large corporation and it was built on flat file CSV database. It worked very well. So well infact that while it was ment for a temporary solution while their IT department built a robust system (designed for 3 months operation), that the system is still in place today!
Flatfiles are good, but it depends on the information you're pulling. Also, flat file are not relation tables (unless you're doing multiple files). It's pretty difficult to write a Many-To-Many script using flat files.
With the speed of MySQL Idon't even think about it when I'm making scripts these days.