Distrust of the Web PKI (the Public Key Infrastructure for SSL/TLS on the Internet that basically falls out of what the Netscape Corporation built in the 1990s) was high and lots of people were sure better was possible. Moxie was one of them and so was I.
So - what happened? Maybe somebody wrote a good article summarising, and will link it here, but otherwise here's a brief summary in two halves, plus a bonus
1. Web PKI trustworthiness improvements. The CA/B Forum Baseline Requirements have been tightened up somewhat, so that the accepted minimum standard is higher than it was. Google's Certificate Transparency work ensure we (the public) can see what they're up to, rather than relying on rumours and guesswork, and so we can insist they do what they've said they would before disaster strikes. The Mozilla project's mozilla.dev.security.policy, open to the general public, began to take its oversight role more seriously.
2. Alternatives proved trickier than anticipated. e.g. Pinning sounds great, and it works for Google, Apple, Microsoft. Most of the time. But it's a massive foot gun, and in some forms (HPKP) it's also a ransom mechanism; DANE leverages DNSSEC, but when you try to do that you find that a surprising number of users don't have working DNSSEC, indeed their DNS doesn't work properly even without DNSSEC; TOFU approaches which worked great for SSH in practice turn out not to suit the way ordinary users interact with the Web.
Bonus: Some fraction of the people who expressed concerns like Moxie turned out to mainly, perhaps unconsciously, not want to pay $$$. Let's Encrypt almost incidentally (because it's automated and machines don't have wallets) is free at the point of use. It's surprising how many people who were absolutely certain they hated the Web PKI in principle came around to it once it was free...