No, I never feel guilty. If they worked overtime I'm pretty sure they would expect to get paid for it. Also, what do you think would happen if the average Joe, working in the average Job, got their paycheque LATE? Holy Hell would break lose! Why should YOU get paid late? It's not right. You do important work! KNOW YOUR WORTH!
YOU need to stop the guilt. As long as you have a guilt mindset people will take advantage of you. And that is exactly what is happening right now. Sure, you are charging them late fees but they are STILL arriving late for pick up and paying you late - in short, they ARE taking advantage of you. Stop that - TODAY! Only YOU have the power to make people treat you what you are worth.