Most of the people that come into the city to shop or dine are not driving in at 8:30AM and leaving at 5:00PM. They, presumably, aren't the targets of the Congestion Toll. And if they were planning to travel during those times, they may change their behavior for these non-essential trips (Voila! The toll worked!!).
People coming into the city for business don't really have a choice. They can either change their behavior (commuter rail, MBTA, rearrange meetings, etc.) or pay the toll for the luxury of spending less time in traffic (again, the toll worked!!).
And spare me the, "Businesses will all move to Waltham" routine. Office vacancies in Boston don't spike every time the Pike toll increases.