Civ III and IV got one great feature - AI NEVER let his transports move without protection, even if transport in sea seem alone then there is a submarine with him. So it fails any logic that transports are moved without protection in galciv II. Lately ai begin to assemble fleets with transports but that's a little help cuz at the beginning you can add n+1 levels on defenseless AI transports that just move to your worlds even if there ships orbiting. Why not just send some escort ships that would move with same movements speed.