Who's funding the S3 bill? Took a peek around crates.io but didn't see anything about it.
Ah, neat! Works out well for them; I assume it's relatively cheap to just serve an S3 bucket on their CDN (though I guess bandwidth costs may rise rather dramatically if Rust ever reaches Node levels of popularity), while not taking on any other operational expenses of actually running a registry.
CDN bandwidth by nature of the reach of Cloudfront will mostly be offload onto the local peering fabrics. It basically costs nothing in per mbit billing - e.g. linx https://www.linx.net/wp-content/uploads/2017/10/Fees_Schedul.... 100gb hand. That's not to say there aren't other major costs in running a resilent edge network which go someway to justify 0.0Y/GB pricing where Y varies from 1-9 depending on location for non sponsored projects. tl;dr - it won't ever be a problem
Note that the crates.io index is just a single git repo that holds JSON metadata about each crate: https://github.com/rust-lang/crates.io-index . The actual code found on crates.io is hosted on S3. The index is an important part of the system, but there's nothing tying it to Github specifically.