In Tudor England, there were times when Protestants / Catholics were persecuted more than, say, Jews. I know very little about contemporary politics, but that conclusion doesn't necessarily follow.
Yup. Historically, because of a long tradition of practices such as jizya, historically (now it varies from country to country) there tended to be much more tolerance of "lateral" religions such as Christianity and Judaism in muslim lands than other sects of Islam, which were considered dangerous heresys. South Asia was kind of unique because there was often muslim sultanate leaders over very large non-muslim populations, and that forced a sort of realpolitik tolerance.
Increased taxation (and, yes, even slavery) is sort of tolerance when compared to war and genocide. If you can enslave somebody as a punishment, you're treating them as free otherwise – treating them as a person by default.
In other times and in other parts of the world, not even that has been the case.