I'm assuming that you got the caliper bracket off?? Rotors like to rust on. There are a couple ways to get them off, you could hit them on the friction surface with a hammer (if not worried about saving them this works well, if you want to keep them in good shape use the hammer in between the studs instead) and if they still are being stubborn use some pb blaster on the hub and the stud holes to loosen up some of the rust and then reuse hammer.
Once removed make sure to remove what ever rust might still remain on the hub otherwise the rotor will not seat correctly and cause vibration later.
Good luck!!
