Hi,
Beginner's world is quite different from "classic" GW. It spreads on much much less time. And there are much less airlines too, and that's probably the reason you're able to have so many flights on the same route (do you have any competitors on this route?). In this case, the limitation sucks, yes.
But on the other hand, in other GWs, it's only intended to limit one's control on a route, so that others may fly it too.
The balancing in the game is calculated to allow enormous airlines, but also to allow to compete with these enormous airlines. If the first big boy in place puts an unlimited number of flights on a certain route, then you almost have no choice but to choose another route. So it's only meant to allow more players to play.
On the third hand (

...), fly bigger planes on this route and you'll take all the demand. Look at real life. Is there 40 flights/day w/ Q400 between Milano and Rome?
Regards,
Arthur