Most global distribution systems (GDSs) rank "direct" flights above connecting flights. This comes from the days when enroute stops to refuel were common, and passengers might genuinely think a stop like that is different/better than a true connection. But now, airlines just abuse the system for the most part. There are a few flights left that might fit the old mold (e.g. the stop in DKK enroute to South Africa), but mostly it's just trickery.

Btw, they also screw you on miles for these flights, only awarding miles from initial departure point to final destination excluding the intermediate stop.