I do not think that there is any significant amount of true, subliminal brainwashing going on in either seminary or in college; there is simply a certain worldview being pushed. And there should be; arguably the most important goal of a school is to ensure that the its students have the proper worldview. The obvious problem is that different people have different opinions as to what exactly is the proper world view. However, to insist all seminaries as “brainwashers” merely because they espouse a hashkafa that you disagree with is intellectually dishonest.
(Also, the argument can be made that the little true brainwashing that does occur in schools is largely accidental. When a teacher says “when you go to college, you will see the full extent of this concept” odds are that he is not intentionally trying to brainwash his students to go to college; he is simply speaking from his assumptions.)
Now, I do agree that the BY system should be more open to answering questions, and should perhaps inform its students of financial the realities of kollel life; but that doesn’t make the entire system “brainwashing”.