Flat files are quick, and require less specialized knowledge to work with.
Relational databases (e.g. MySQL) are easier to search through.
Says Patrick Michaud:
When Wikipedia rose to dominance, MediaWiki became the default standard. It uses a relational database.Patrick Michaud wrote:I chose flat files to store PmWiki pages because I haven't seen any real advantages of using a database, and there are definitely some disadvantages. For the standard operations (view, edit, page revisions), holding the information in flat files is clearly faster than accessing them in a database, and with page caching abilities (coming soon) it'll be even faster. The only operations that really benefit are searches, but I've always believed that for fast, flexible search capabilities it's much better to use existing search programs such as ht://Dig or Google over reinventing another search engine. PmWiki's Site.Search is functional/fast enough for most purposes, and if more performance is needed it's just better to switch to a real search engine.
Fast forward to 2017, and interest is growing again in flat file storage. Funny how ideas come back like that.