You have no right to attack a transport that isnt in alaska, z-21 or your gaurd system unless it is attacking you (shields down 50%) of it is feeding other ships that are attacking you with bots/bats.
The rules need a revision to prevent misunderstandings in regards to these situations, but until things are cleared up, just avoid shooting transports in a cap unless it is absolutely vital to your ships survival, and you have evidence to back this up.