The problem with making it easy for website owners to deploy encryption is that it also lowers the entry bar for cybercriminals. Buying TLS certificates to encrypt malicious traffic didn't make much business sense for criminals, because they typically switch domain names at a fast pace to evade detection by security companies. But now that certificates can be acquired for free and in an automated manner, security solutions will likely have to deal with an increase in malicious encrypted traffic.
However this will play out in the long term, the general thinking is that improving everyone's security and privacy by widespread use of encryption on the Web outweighs any potential risk of attacks becoming harder to detect.
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