The boys at MLCO, at least on the Private Client (PC) side, make money in several ways. One, for each product they sell, they take a front-end or some other kind of load. Two, they also receive a trail from anything they sell, so, they continue to get paid even if they do not sell new investments to a client. They just need to keep bringing in new accounts to keep the gravy flowing. Three, they try to put clients in MLIM funds, so as to keep the money totally in-house. Four, any accounts under $100K are farmed out to a call center, so the FAs can concentrate on hooking the big fish. So, with a front-end, level, or back-end load, a trail, and a management fee all going to Merrill, it is a wonder the client ever makes any damn money. Please note, I did not even discuss traditional commission based business (other than the loads).
They also have discretion as to how much of the Financial Advisor's (FA) portion of the fee they can discount down. There is a greater ability to discount products that have a larger overall fee, i.e. Mutual Funds. Merrill has also been pitching itself as a one-stop shop lately. I believe they are doing this to sell the customer on the perceived convenience of their "overall experience". As one might guess, this convenience comes at the cost, from the client's perspective, of losing the most competitive (READ : lowest) fees on each individual product.