As much as I love John Oliver, he gets some things wrong and this is one of them. Honestly it's a bit frustrating as he's clearly going for the punchline more than accuracy. Fact check everything from that show.
A ton of air routes go over regions with local tensions. It's industry standard, and has nothing to do with Malaysia Airlines. Airline routes take a very long time to set up.
Wikipedia has a map will all high tension and ongoing conflict regions.
Here's an airline route map from 2009: