What is wrong with giving money to places that make learning Torah  into a business is that when you pay people to learn Torah for money, there is no room for people that learn Torah for  its own sake. This is a well known and documented phenomenon. I have heard and seen this plenty of times. If some one wants just to sit down and learn Torah without getting paid for it but just for its own sake there is almost no yeshiva that will not throw him out. It is a outrage but it is a fact and woe to the individual who brings attention to this.

I am not trying to make a halachic kind of decision here. This was dealt with by The Rambam and Beit Joseph and later on people. To the Halacha side of this issue I have nothing to add. But to the practical side of this I have a tremendous amount of facts that show that surprising people that use the Torah for money only hurts Torah. Support for the frauds makes things hard for sincere people.

When Reb Chaim from Voloshin started the yeshiva movement the way things were that the synagogue was used as a study hall during the day and was connected with the local Rav. Reb Chaim changed that to the new paradigm of a yeshiva as an independent institution. This was a good thing but people started seeing that it is a good business. And that ruined it.