Transports provide protecting from snipers and a lot of other hostile ships, immunity to mines and tractor beams (making them invaluable with permamines), and are in general useful in a lot of edge cases (against planetary cloakers, for example, or for sneaking some of your low-level ships past a high-level enemy planet).
Unlike a lot of other strategy games (SupCom) where transports are used primarily for a speed boost and to help ease logistical troubles, transports in AI War are almost entirely about bypassing dangerous things that are otherwise impassable.
There has been some talk of some higher-level transport ships, which would have things like cloaking, etc.
