Because people end up watching Fate/Zero's anime which actually did bastardize Kotomine's character by changing the events and subtexts of the shit he does without giving the actual subtext either.
To put it more bluntly, Kirei Kotomine actually IS religious and has a moral center and it's precisely why he hates himself so much. What ultimately made him become evil wasn't Gilgamesh goading him, but him wanting to kill Claudia despite her hoping her death would get him to feel bad for her. To put it plainly, Kotomine is someone inclined towards evil, hates it and wants to be good because that what he was taught and he hates it.
To try and act like Kotomine was never religious is the understatement of the year as he is a genuine priest with genuine faith and THAT'S the entire point of what his wish truly is in Heaven's Feel:
Why does someone like him(Someone who was born evil but was able to gain a consciousness) was even born which in a sense, is the equivalent of asking God why you exist.
So I can see why people can believe that because well Fate/Zero may be a good anime to start Fate with(HA!) but it's a TERRIBLE adaptation and there's a reason why Nasu even at the start of the Volume disqualified it as a Timeline connected to the VN which still holds to this day(To many Fate/Zero fans chagrin).