What do you have in your contract?
If you don't have a contract then that's where to start.
And there's no such thing as rates you or anybody "should" have. And discussion of prices amongst professionals within a professional channel is a huge no-no. This is always a good place to start working out your own rates: http://freelanceswitch.com/rates/
I know that others have also mentioned various equations they utilise. But it all comes down to what you value your time as, and what costs you have to cover, nothing to do with anybody else as we all have specific circumstances.
I charge at an hourly rate and all changes are included in this. Personally I give each client approximate quotes which are usually spot on due to doing similar projects many times - so that's just down to experience.
The only changes I don't charge for are ones small enough to not warrant my notice eg: small word change then re-pdf (5-15 minutes).
The thing about changes is that they are part of the project, so until the file is at the printers or on the net, then every change is part of the creative process - and so is chargeable.
Limiting changes is also a skill that you learn over time. Communicating with your client right from the get-go to ensure you are both on the same path stream lines the process... then again, clients can sometimes say one thing and want another giving you a brain aneurysm - one of the wonders of design work ;)