There are many collectable flags throughout the game of Assassin's Creed and every time one is collected, you get a progress indicator (e.g., 33 of 100). Is there any reason to collect these, other than bragging rights? I recall getting all available flags in one particular town and never saw any special reward or secret revealed.
The point is only to get the achievement. You don't unlock anything by collecting them.
There are 4 achievements associated with flags: