I'm new, and as I look trhough many advanced fleets, I see at least one and normally two of those transport ships, but I don't see much in them, could someone explain why they are such a valuable choice in high level playing?

They are cheap activations is the short answer, which gives you much greater flexibility as to when you activate specific ships of your own, as you can delay activating specific ships by activating these instead. They are also excellent for pushing squadrons around with squadron commands (and are a very cheap way to do this, and you really don't want to be using your big, heavy hitting flagship to be moving squadrons around a lot of the time), and the fleet support slots can give you some interesting additions. Comms net, for example, is a great one for spreading tokens throughout your fleet when your main ships need to be doing other things, and a bargain at only 2 points.

They will do little to no direct damage from fire, but the ability to "out-activate" your opponent, is not one to be sniffed at.