You don't pay more to use a travel agent. The commission is paid by the cruise line. We have many agent members here, who can explain it in more detail to you. However, one thing to note is that if you call a cruise line directly to make a booking, it is quite possible the cruise line employee you talk to is also paid by commission and not strictly a salaried worker.
I always use an agent, and in fact I have filled the role of an agent a few times under the blessings of my agent - making my own bookings. In fact, I plan to increase my participation in this soon and may eventually be considered a cruise agent myself.
An agent is more than someone taking your order. They are an advocate for you, which may not always be true for direct bookings made with the cruise line. My agent takes care of me. When prices go down she gets me a refund for the difference credited to my booking. I don't have to ask. She gets me shipboard credits and other perks. And it doesn't cost me a penny.