Can i paint rust-oleum protective enamel over kitchen cabinets that have stain on them?

Yes you can. Take a medium grit sand paper and rough up the finish a bit first to help it stick, then if you are just spraying clear coat over them, go at it. However, it is very difficult to keep it from running. I always prefer a brush on finish for cabinetry. If you were going to spray them a color, prime them first. If all you are looking for is a clear coat, it is best to apply a polyeurethane with a brush and then sand it lightly with a fine grit paper, then an ultra fine grit for a nice glossy finish. Unfortunately, there are no short cuts if you want it to look nice.