The major place where the Rambam is critical of the yeshivas in his time is in his commentary on Pirkei Avot דאשתמש בתגא חלף. ["One who uses the crown passes away."] [Not in the first place in Pikei Avot where this statement comes up but later in ch 4.] So he would not have been very happy with the kollel system. And even today it is a major shock to read what he wrote 800 years ago and basically is still impossible for anyone to swallow. He holds that (I am paraphrasing) the heads of the yeshivot that say it is a mitzvah to give money to support these institutions are liars.
There should be yeshivot where people learn Torah, but they ought not to be means of making money.
But in his own days, the implications of what he wrote were clear to people and caused the first major controversy.
He was dealing in this from strictly a legal standpoint, but I think he also saw some of the implications of using Torah as means to make money. One implication is the ruin of Torah. Or rather-the ruin of sincere Torah. Those that are sincere are despised.
