In theory, the agents used to get (may still do) advantageous rates for hotel rates either via the tour operators or hotels directly and that was how they made their money plus whatever mark up they could put on top. This model can still work, maybe not by offering the cheapest holidays but by offering exclusive deals not easily available on the net.
I was on holiday earlier this year, in a cut price 5 star hotel (4 star UK standards), but only went B&B because the all-inclusive deal was just buffet style and I've done that before and haven't been impressed so went out every night to the dozens of good eating places nearby. I thought at the time why don't the travel agents build up deals with local quality restaurants near to hotels to offer a sort of all-inclusive package and throw in excursions to sights and theme parks and all the other things you can do, transportation sorted. Fully managed trips that are hard to do arrange over the net. That's the future I reckon.