Moral of the story: only use SQLite for websites where updates to the database happen rarely (less often than every page loaded).

Think about indexes:

As I mentioned in my first edit, database indexes dramatically reduce query time, but this is more of a general observation about databases than it is about SQLite.

And transactions to speed up writes:

However, there is another trick you can use to speed up SQLite: transactions. Whenever you have to do multiple database writes, put them inside a transaction. Instead of writing to (and locking) the file each and every time a write query is issued, the write will only happen once when the transaction completes.