You should ask Michael Saylor to be sure how he proposes this will all work, but he did mention his company (MicroStrategy) spends $1M/year on DDOS mitigation. I expect if Lightning ends up as cheap and fast as he and others are saying it will be, it could be funded by companies as a cost of doing business in the same way they fund the electricity and hardware for serving their websites.

It's actually the sort of thing I could see CloudFlare etc. providing, so each website doesn't need to implement it themselves.