I, as well as every other DWB, had the same questions at some point. They are charge more because it takes extra work to set up a meal for that many people. For us, they closed down the whole restaurant and had additional staff, extra special drinks, music, etc. I also think they just do this because it's a good way for them to make more money. You'll notice, the resorts charge a ton for things like flowers, chair covers, runners, candels, cake toppers, etc. It's their way to make money - they know that you are (probably) in a foreign country and can't just walk down the street and get your services another way. They know you're forced to go through the resort and they'll make you pay for it It's all worth it though! And there are many ways to save $$$.
On another topic, if you're looking to save money, one thing I'd advice against is the group travel option. Often times the company booking your wedding will give you a deal, or offer so many free meals if you travel as a group. DestinationWeddings does this, along with many other destination wedding wholesale companies. Traveling as a group means all your guests have to have the same departure city, room category, number of night stay, etc, which I think limits the options for your guests. I think they are traveling all the way there for you, so you should allow them the flexibility of traveling whenever and from wherever they'd like. I know you might loose the "free" meals, but I'd take money from somewhere else just not to force your guests to do something they don't prefer. That's my two cents