Depends on the intent of the author.

It doesn't bother me when JRPGs have evil Catholic churches and where you eventually fight and kill God because I know they're just looking for cool motifs, and barely understand the religion they're riffing on (in the same way they use Norse mythology in games - it's all just "foreign myth" to them).

I find stuff like the Golden Compass annoying because Philip Pullman comes across like a bitter dick with an axe to grind, who is deliberately aiming at children to influence young minds.

If you're writing as a "Gotcha! Fuck you!", you're probably kind of an asshole. The same applies whether you're basing your main villain on the guy who cut you off in traffic or your ex who left you for a guy named Serge, or if you're taking shots at the church because you're still mad your mom made you go to Sunday school as a kid. It's just petty and sad.