Fleets insure that all ships stay in a formation. This means that as many ships as possible will all be firring at the same time. Instead of having each ship fly around on it's own and when you give the order to fire they each fire when ready, a fleet will be all firing together as much as possible.
There is a big disadvantage to this which is speed. Fleets can be very powerful in certain situations but if the enemy can stay out of your range then he can safely pick away at you.
Fleets are most useful assaulting defended posititions. You know you're going to take damage from the defenses and you want your forces to do the most damage possible while receiving the least damage necessary.
In general combat fleets are more of a burdon. I rarely use them because it makes all yoru ships move so slowly.
I'm not sure if there are bonus's built into fleets? Maybe i'm just not aware of a boost to some stat that fleets get. The loss of mobility is a big deal in most games I play. I'm going to play with fleets, maybe I'm not using them effectively.