I think providing a means of indoctrinating future generations isn't charity by any stretch of the imagination. Now, if they actually ran totally free secular schools with no religious instruction whatsoever in poor neighborhoods which accepted everybody no matter their religious beliefs that would be an entirely different story.
I can tell you what happened in my experience in Catholic parochial schools. During my primary education (one year, eighth grade) attendance at religious events (ie Mass) was mandatory. I don't recall whether participation was mandatory; I don't think it was but it was certainly expected. It was generally expected that you were Catholic if you were going to that school. Catholic values were integrated into many parts of the curriculum and were stressed, but did not overshadow actual education. I think religious education classes were mandatory. After an unpleasant incident, my punishment was to sit in front of the statue of the Madonna and mediate and pray about my actions.
During my secondary education (all four years), attendance at religious events was mandatory but participation was not (since these were whole school events this makes sense from a safety standpoint; you can't have some children absent from a whole school event very easily). Indeed, the school would often invite in clergy from other faiths to participate in important Masses (such as before Easter, Christmas, and graduation). Catholic values were present, but not stressed except in cases where they illustrated an ethical point. In general, the actual values were not solely Catholic but instead generally mirrored common ethical standards. Religious stuff didn't enter into academic education; in one incident a classmate of mine raised the question of creationism during biology class--he was pretty much laughed out by the teacher (it's worth noting that Catholicism accepts evolution as a physical fact, but the teacher made it clear he was teaching science and not religion). Religious education was mandatory for Catholic students only; students of other faiths could opt out of religious education. It was not assumed that the students were Catholic and no effort was made to proselytize to them other than attendance at Mass. Contentious Catholic values, such as the ban on abortion and birth control, were not stressed or forced upon the student body, although it occasionally came up in religious education in a "by the way" type way.
It is worth noting that my primary education and secondary education took place in two different states. I grew up in a some what rural town and then went to high school in a small city. This may account for why the secondary education was less Catholic focused and more cosmopolitan, but I would assume that my experiences are likely similar to others who attended parochial schools.
When I attended (public) college, I found that my grasp of various academic elements was superior to many of my peers who attended public school. I credit this to the value of the parochial education I received.
I am almost certain that students attending Catholic colleges, such as Georgetown or Notre Dame, are not obliged to attend any sort of religious service, although I'm sure that religion is integrated in various ways, such as through opening prayers and the like.
An education at a religiously funded school does not necessarily mean that the students are being indoctrinated. That said, how a parochial school operates differs from how schools operated by other religious work. There certainly are schools run by churches that really indoctrinate their students. That said, I would not be at all surprised if other religiously supported schools, such as Quaker schools (for example), have even less focus on religion than I had during my education.
