That is simple economy, more supply than demand = lower revenue/lower profit. In this game is more competition than in real life and airline must look at it. If you will be making multifreq routes and will be competing with big airlines they will be using big planes and price will go drasticaly down and you will be not making mostly any profit and your airline will be going to bankrupt.
Not to mention, those same airlines not only have larger planes most of the time, but also more of them to place on the same route, and could even afford to lose some money on a few routes, just to sweep out the competition. The game used to have a problem (fixed years ago, but I was playing my first rounds at the time) where people would have all of their routes to .5s. It caused quite some controversy early on, but was fixed in the end to where each aircraft could only have 2 .5 frequencies only.
I do have a feeling though, that having the code making an "optimal" amount of frequencies to max out the demand may cause another Pandora's box of sorts to open up. There was an other very similar game that worked a lot like that (and many older players of this game were very likely players of that game too). When I last played, a typical 10 year round went like this: year 1 and 2 were productive for everyone, people were getting their first Airbi and Boeings. By year 3, the larger guys would really start to build up, by year 4, the top 5 or so had basically taken over most of the routes, and no one could afford to make a decent profit. Admittedly, Airline Mogul forces the Hub and Spoke system more, where this one was a bit more free, and didn't require Hub/Focus City to be one point of the route, thus allowing such domination to take place. Of course, to add, that game also had a different profit function too. In that game, a full plane was not as profitable as a plane with like 2/3s of the seats left. Of course, all the insane problems with that game is what lead to this game being created.