I find that during development it is of great benefit to have configuration stored in a file.
It is far easier to check out a file (web.config, app.config, or some custom file) and make changes that are instantly picked up when the code is run. There is a little more friction involved in working with configuration stored in a database. If your team uses a single development database you could easily impact other team members with your change, and if you have individual databases it takes more than a "get latest" to be up and running with the latest configuration. Also, the flexibility of XML makes it more natural to store configuration that is more than just "name-value" pairs in a file than in a relational DB.
The drawback is where you want to reuse the configuration across multiple apps or web site instances. In my own case, we have a single config file in a well-known location that can be referenced by any application.
At least, this is how we store "static" configuration that does not have to be updated by the system at runtime. User settings are probably more suited to storage in the DB.