How do for-profit Incubators make money?

There are many types of incubators, and the only accurate answer for all your questions would be, "Depends." But that is not helpful at all. So, let me take a stab at your last question. In every incubator that I have come across (though I exceptions can be found), the real money will end up getting made only upon stellar exits. Given the increased competition in the incubator space, incubators are not able to maintain a positive month-on-month cash flow. This is all the more true in cases where non-profits, community organizations, universities and the like run incubators.
 
There are incubators that are really business centers disguised as incubators. They do not take an ownership stake in the incubates and only charge a fee for the services rendered. These kind of "incubators" target being cash flow positive at all points of time.