This is precisely why it's important to make these tools (protocols/applications) part of the core layer of how businesses operate consumer-facing services online; it's only true if the ratio of "interesting" communication over these channels is high enough.

In an alternative timeline where ISPs where more strictly regulated and trusted and everything was cleartext HTTP, I'm certain that HTTPS/TLS would face pushback from regulators. There's no way it can be banned today, though. Similarly, you won't be marked as suspicious just from opening an encrypted TLS connecting over port 443 to an arbitrary endpoint.

I don't think it's too late. There is a significant probability that today's centralized incumbents will Myspace at some point in the future. These federated, decentralized and secure solutions could be the next iteration after that.