If the Transports get intercepted then they usually only take a little damage and you can always retreat them.
The problem is that you can use Paras again and again in rapid succession to take large amounts of terriory in the enemy's rear.
Fed 3.2 made them much more expensive to produce which is one option. Another is to make them lose Org a lot after a drop but then they would lose most fights.
I personally only use them to do a couple of historical missions (like Crete) and after that just have them on the front line.