His motivation is religion based. I bet you can already see the problem.
So basically he was raised on the idea that society and most people in general are impure sinners that just breed more impure sinners, so he grows up thinking "I'm gonna do something about it". So, y'know, naturally he commits genocide/mass murder /s (I'm not sure which one it would be considered.) He just a-bombs like most of the world and then tries to kill off the survivors via disease and virus.
He's obviously beyond extreme and evil and I have other religious characters that are very pleasant and good people, but I'm still worried about offending any religious people. Is this something I should change?
In my opinion, it's okay as long as he's not doing it in the name of any particular religion because that can spread untrue and harmful stereotypes that are already very prominent in real life. Of course, I can't speak for everyone. If you've seen death note he could have more of a complex where he thinks he is god and has to get rid of all the sinners for a purer world, like Light does in death note. Or where he's playing god because in his eyes he's making the world better.
I agree with the previous user that said naming an IRL religion is more offensive. Having religion/belief/superstition be the center of an antagonist drive is not at all a problem. It occurs more than you might realize because what is at the center of their thoughts (impurity) is a theme found throughout a lot of literature. Characters acting in a way to rid the world of sinners/evil reflects real-world conflicts led by religious institutions or believers. At the end of the day, you're writing about a person or group of people who believe they are making the world a better place through violence. It is not the consequence of them being religious in general (as you feared) but rather the manipulative nature of that institution.
Your story is fine. In fact, if you're looking to make religion and manipulation the main point of your story, you can look at Niel Gaiman's American Gods.
Granted, if you are doing it on an island religion that you belong to (and have other good characters that belong to it), it should be fine as well.
Thank you all so much ! I wanted to keep the same premise but I couldn't think of any way to change it without changing his whole motivation, but your suggestions help a lot. I just started the 1st chapter so the villain hasn't even been introduced so it'll be a super easy change. And I think I'll also have more flexibility with his backstory too instead of just extreme christian family.
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