Yea I never got transports either. They did not seem that defensable, and there speed was slow. Pretty much as slow as your slowest ship. It always seemd better to move my fleet in a blob. Sure I might loose a few ships, but I am going to kill some too.
There is only one advantage I see to using transports. Moving your fleet closer to the desired target, without the AI being aware and sounding the alarm. But my play style does not worry about this, or I work around it so transports are worthless to me.