They may not be religious, but many borders (probably most of those which aren't due to the natural geography?) are the subject or result of some kind of conflict. So is this border really that special? Probably most borders in Europe were the subject of conflict within the last 100 years, but we've ended up with the Schengen agreement nevertheless.

I think this is a very recent conflict. Not over the border exactly, but between the religions.

It's been going on for over 400 years:

http://en.wikipedia.org/wiki/Segregation_in_Northern_Ireland