The jesuits were simply too competent. Yes, the spanish crown had a great deal of independence form the vatican -the "Spain control the pope" is an exageration, actually; they simply ignored him when it suited them, and they were too powerful for Rome to protest (too much). Basically, they had what Henry VIII wanted.
But just because Rome had no much power, if does not mean than the Crown controlled the church. The spanish church -most the churches, actually, but it became very clear in Spain- were a real meritocracy in a time where aristocratic nepotism (and incompetence) followed the norm. It had its share of nepotism, but is was maily centered in Rome (corruption on the vatican was the main cause for the Protestan reform).
Spain had very intelligent and learned churchmen, with, by the time they were in a position to meddel in mundane politics, a lot of experience in the church political infighting. By contrast, the nobles had their position because their daddy got them. For that reason, the spanish church had a lot of real power.
As the centuries went, the power -and arrogance- or the church grew, and its competence lessened, so the kings decided to cut its power at the knees. The jesuits were the more visible and powerful order, and they were expelled from spain in 1767 (they would return later when the king power and resolution proved temporary, but later in the nineteenth centurry the churhc lands would be "nationalized", again mostly temporarily).