It's not so much a problem for me that the trucks and trains are weak cause they usually operate behind the actual front. But the real disaster is the amphibious ships and the planes.
Anyone who has played the sea lion campaign knows what I'm talking about. Before you get to land you've usually already lost about 10 of your troops (or even more) to enemy naval or air fire (and in the norway campaign there's that pesky fortress..).
I've played PG2 for a long time and there the ships only took 1 or max 2 damage when targeted. In PC they take like 8 from pretty much any enemy fire, whether it's destroyers, bombers, artillery or infantry on the shores. Against a somewhat decent fleet that's gonna get you into a whole lot of trouble.
And postponing the invasion isn't really an option either with such a strict time schedule

The paratroopers are equally hard to use. Even if you protect them with a fighter the enemy aircraft still do 7 or 8 damage everytime they attack the plane these brave fighters are in. And a 2 or 3 HP paratroop stranded in enemy territory isn't likely to last another turn to reinforce.
Basically the fighters are doing a pretty damn poor job in protecting weaker air units. Even the (protected) bombers are easy targets when attacked.
I'm also not really sure how to use my paratroopers. They are too weak to capture any half decent defended cities and airfields are pretty useless (you can't really fly in more troops by air because they will have to fly in the same 'coffins' as their predecessors).
So yeah, I'm a bit at odds here.
It would be nice to get more defensive support from fighters. And with regards to the ships. Maybe the current damage can be reserved for ships that are adjacent to the shore (as signifying embarking/disembarking troops), while ships further off shore are considered as large transportation ships (and thus made less vulnerable). The ports could be places for these large vessels to safely unload their troops without turning into weak amphibious vessels.