Are there any well known anime characters that are Christians?
Let's see if I can't dust the old anime locker for this question... Here I'll attempt to name main and iconic characters in answering your question. I'll also try to aim for those that managed more than a niche following along most of the fans outside of Japan, but no guarantees...
- Chrono Crusade - The main character Rosette Christopher is part of an exorcist group, the Order of Magdalene; which is in turn headed by the Council of the Catholic Church. By extension you could say that she is a practicing Christian, but it's been awhile since I've read/watched this (rather depressing) series.
- Hellsing - Here we have Alexander Anderson, the main antagonist to Alucard and part of the Iscariot Organization, also known as Vatican Section XII. He is for defos, an ardent Catholic.
- Trigun - Nicholas D. Wolfwood, who is one hell of a badass character by the way, is a priest in the series. Interesting to note also is the fact that the author/mangaka Yasuhiro Nightow is a Christian convert.
May add more if I remember, but yeah. These were some rather significant Christians in anime.
Keep in mind that anime writers don't treat Christianity any better than they treat shintoism or other religions - i.e. they will happily use them for visual, conceptual or comedic flavor, but they rarely (if ever) bother to have any sort of authenticity or accuracy in the process.
In other words: Better don't expect Christians/nuns/priests in anime to do any nun-ish or Christian-ish things. Simply put, they have their religion mainly to get access to the various "cool" paraphernalia or concepts that come with it, not for conveying an accurate picture of the religion itself.
With that caveat out of the way, there is indeed a sizeable bunch of catholic priests featured in anime, though they are somewhat less common than their distaff counterparts. Most likely due to being not nearly as cute-y-fiable.
But there's at least one pretty prominent badass that every anime fan worth his salt should definitely have heard of - Kotomine Kirei from the Fate/xyz universe.
Dunno about "well-known" - most of the well-known ones are questionable Christians because their writers basically used the outer trapping of Christianity, but not the actual beliefs. The "violent priest" archetype like Wolfwood in Trigun isn't exactly all that Christian (though take note of that ending). Since the list of well-known ones is so short, I'll give you a few less well-known actual Christian ones in addition.
Samurai Champloo has a (historically accurate) subplot featuring a group of persecuted Japanese Christians, one of whom is important to a main character.
Katou Saint Tail (Mysterious Thief Saint Tail) has a main character, Mimori Seira, who is a nun-in-training. The protagonist also prays (with folded hands) before and after each transformation.
Sakamichi no Apollon (Kids on the Slope) has two main practicing Christian characters - not just the outer trappings of crosses, but two church-going Christians. One of them later becomes a priest.
Rurouni Kenshin (Samurai X)
Anime has a "Violent priest" archetype which occurs fairly frequently.
For example there is this guy from Hellsing:
Off the top of my head, Zakuro Fujiwara from Tokyo Mew Mew is a Christian (although the dub removed this); so is Inori Yamabuki from Fresh Pretty Cure. Also, this series isn't exactly well known but its contributions to the yuri genre were important and it is set at a Catholic school: Maria-sama ga Miteru. The majority of the cast is Christian, and there are many references to religion - the series name even means "The Virgin Mary Watches Over Us".
Hope this helps!