I suppose the reason is that you have no chance to drop loaded units on water. So the developers wanted to give people flying over water with trans a chance not to lose important and expensive units. Flying over normal land you can always drop the units if you can see enemy planes upcoming. I would even prefer that in general landed transports cannot be target no matter if water or land. Transport planes are shot to easy in my opinion. It would be a nice option to create stable "bridges". You need a bomber or a land unit to destroy it if it is not in use. If a lot of tanks coming there ot be transportet you can sent interceptors.
I created already another topic about transport handling and i think that transports or at least ferry comands cannot be used good enough since the planes are shot to easy. i was suggesting to be able to make ferry commands without planes. But while thinking about the problem you are discussing here i think that would be even better
Just taking an example of the map eiertanz. I conquered the third island and had a big outpost there with 3 factories. Next to the river i had an aa gun and several transports as a bridge. As long as this is not used it should be save until enemy ground units destroy it. Atm the enemy just flies by and everything is dead.
A possible solution atm for me would be to make my transport lines all starting from lakes and rivers and let the planes fly the way to the tanks then.
p.s. UEF t2 gunships can carry units thats why they have the same behaviour