If you were using large files, flat file database might not be the most appropriate way to go. I've never used flat file in PHP, however, way back in the early days of perl before MySQL was widespread, I remember how incredibly inefficient flat file databases were. They were great and quick for very small databases. But once the files got larger, it became problematic. It was this very problem that eventually forced me to learn MySQL.
So with MySQL so readily available and widely used these days and supported in PHP, why work with flatfiles at all?