There are different uses for both, but generally 'I can't help you' means I am not able to help you at all. Perhaps the person doesn't have the skills or ability. 'I can't afford to help you' more suggests that there is something external preventing the person from helping. For example, if there was a risk of getting in trouble by doing something in a workplace and the person really needed the job they might say 'I can't afford to help you' as in, I would like to but I can't risk my job for it. Or if someone asks for money and the person doesn't have any, they might say they can't afford to help.