I saw a neoprene carry bag for laptops; maybe something similar would work for the Kindle?
Here in Australia, as part of the "let's pour as much money as possible into the economy and try to save us from the GFC," our Federal Government handed out free Lenovo laptop computers to every high school student in the country. These came in a fairly robust clear plastic shell which was a snug fit - too snug. The word came out round the schools to stop using those plastic shells because they were so tight that they were cracking laptop screens. So kids are carrying their laptops to school each day using whatever means they can. difficult child 3 uses a fairly soft computer carry bag (on those days when we go in to school - maybe once a month). The neoprene (wetsuit fabric) could be made to order yourself, especially if you are a dab hand with a sewing machine. I've seen wetsuits in poor condition for sale in op-shops, you could deconstruct an old wetsuit and stitch something to order for the kindle. Line it with bubble wrap, if he can resist the temptation to pop all the bubbles!
husband carries his laptop inside his backpack, using an old canvas bag. He uses a padded post bag too, to give it a bit of protection.
Marg