Seems to me they're operating on a matter of principle.
The Christians who run my local food bank do similar. Their clients include some of the worst people: rapists, paedophiles, murders - released from prison, with nothing and no-one to help them, other than these kind churchly individuals. Their principle is that Jesus would want them to help their fellow humans in need, no matter what their sins. So they do.
Obviously it's a bit different with Cloudflare as they're a for-profit company of diversely ideological employees, not a non-profit charity of devoutly religious volunteers. But the former type of organisation can run on principles other than making money hand-over-fist too.