I’m no A&A veteran, but the way I see it, the U.S. and German economies can afford transports, since they’re great powers. Transports are expensive because if you destroy a transport fleet, in the case of the U.S., it’s a major strategic achievement. The U.S. isn’t out of the fight, but you’ve seriously retarded his plans and brought yourself time, in addition to any units they were holding, too. Now the U.S. also has to build those boats back, too.
Japan doesn’t really need/get enough transports to get the eastern islands in the Pacific right away, because first it wants to build up its economy. Once it does that, it’s free to work towards other objectives, like those islands, but with a higher resource base.
Italy and the other nations, I don’t know, though. I suppose destroying too many transports for them is basically too major a setback, so it forces those powers to play more carefully? I’m not too sure.
Anyway, that’s how I look at it.