Transports are used to raid resources from enemy bases. Warehouses are usually targeted as they give a good amount as well as any rare resources the player has. The more transports you send the more ressources you can attain, however, there is a limit to how much resources that can be taken per attack depending on the buildings level.
Transports are especially useful to complete limited time missions (ltms) that involve raiding. Your unit storage research level dictates the number of transports you need to send to take the same amount of resources (rss). Typically sending a wave of 2400 trans at a level 18 warehouse yields a decen haul. Usually any more and you will surpass the limit of the max level warehouse.
---edited by w38---