Hi. Yeah, this is a tough one.
From the words of Tom Brady, if I remember.
You can snuff it out its startup with D+FP or D+FK, if you know its coming.
Otherwise, you can only punish it on block, with a fast uppercut, which only half the cast has, or a fast special, like Raiden's Electric Fly. When countering, watch out for Cage's X-Ray if its stocked.
Cage's placement during the flip kick, determines whether or not he crosses you up on his descend after the flip, this could pose a problem with your countering. From what I understand, if he's point blank, he'll land behind you. If he's about 1 character width or just under, he lands in front of you.
Don't quote me on this, but that's my understanding.