While at first Humanism looks incredibly powerful, people seem to forget that converting also brings it boons.
First of all, the simple base Tolerance of Own Faith alone, without any modifiers, is higher than any stable Tolerance of Heretic/Heathen. It's also much easier to sustain a high tolerance of true faith, while you're sacrificing missionary power, stability cost or monarch points through policies to maintain a high tolerance to heretics and heathens.
Religious is the stable version, allowing for cheaper culture and religion conversion, where as Humanism will forfeit those securities in exchange of never having to convert anything.
Religious is a must for large catholic nations, while Humanism will be great for smaller, expansive nations that'll deal with heathens they don't necessarily want to convert (Genoa, Venice, Netherlands, and most German and Indian minors).
Humanism isn't so overpowered when you realize you're working through a stay-of-execution method rather than a security method.