But the flaw in your understanding of how it works is that first, airlines no longer pay a commission. So unless you want to pay a fee to the agent to do the work for you, you have to do it yourself. But air reservations are different because there are not alot of options or questions involved and they don't stop at different ports for a day. Cruises involve alot more information, especially for first timers who can often ask a ton of questions (and should).
The problem is with most of these discounters, especially the big ones, is that they hire sales people, not certified travel agents, to sell cruises. They have no knowledge to offer the consumer and are pretty much worthless should questions or problems arise. (Generally speaking, of course, as there are always exceptions to every rule.) And, as I said, because they choose to discount, they have to concentrate on quantity and not quality.
So, if price is your only concern, then by all means book with a discounter. Just keep in mind that of all the agencies that go bankrupt, the majority are discounters. Also, plan to do all the work yourself and know if you have any problems, it can be a big hassle. And lastly, look for fees that aren't readily made available. This is important should rates go down - they may charge you a fee to make the change.
It's like working on your own car. If you have the skill, the parts, the tools, and the time, then work on it yourself and save some money. But if you don't have all of these, then it's best to let someone else who's trained do it for you so you don't have to worry about any of the details so you can enjoy a hassle-free vacation.