It depends how hot. the regulators job is to dump the excess voltage that the alternator makes at higher engine speeds so that the voltage stays around 14V and does boil the battery. it dumps the excess voltage as heat. does your design have cooling fins? if not, it must be using something else such as the frame as a heat sink so make sure it is in intimate (ie clean) contact with that other thing or it'll be hotter than it should be.
So, a working regulator will be above ambient temperature, but I wouldn't expect it to, say, burn your hand. if your battery is healthy, then I'd guess your regulator is healthy. Use a DC voltmeter to check the output with the engine running at different speeds and, just for fun, switch the voltmeter to AC to check the rectifier is doing its job of putting out nice, clean DC. You should see roughly 14V DC and zero AC.