Bear in mind that a vessel's protection rating is basically its chance to be hit. This seems to be 5 for a normal object, with the shield's rating enhancing it (the protection rating) by deflecting glancing shots. The shield then protects the ship by absorbing damage as well (the threshold).
Damage to the shield is represented by shield strength, starting at 10 and reducing to 0 when the shield is explicitly down. The shield can also be damaged on its own damage track by criticals.
I thought this was really complicated at first. Then I looked again, and it all made perfect sense...
Jon
"There are worlds out there where the sky is burning, where the sea is asleep and the rivers dream; people made of smoke and cities made of song.
Somewhere there's danger, somewhere there's injustice, and somewhere else the tea is getting cold. Come on, Ace, we've got work to do."
THE DOCTOR, "Survival" (Doctor Who)