I was sent to the Catholic Clonakilty Boys National (primary school), and then to the Protestant Bandon Grammar (secondary). I was only forced to participate in the primary school, with things like Ash Wednesday, by request of the teachers. I found it spooky.
My parents never asserted any beliefs on me. I learned about a bunch of religions in RE in the Grammar. I recall the RE teacher trying to use what I later found out to be Pascal's Wager on us. It almost had my young logical mind convinced! Then I tried it between two religions and it fell apart. Rational thinking is always there when you need it
From my own experience, the religious views of the schools didn't matter. Nor did it matter for my sister who attended a convent. What goes on in the home is what is truly important. My mother defied her mother-in-law when she chose not to baptise us, retorting with "I cannot make that decision for my children, they have to make their own". Just nurture rational thinking, reasoning and logic in the home and there is nothing to worry about.