The major Linux distributions replaced ntp with ntpsec. A better question would be who is still running ntp. I know about FreeBSD and NetBSD.
ntpsec as a project seems to be doing ok. They are releasing new versions, fix reported issues, accept patches, and develop the code publicly. While ntp still has a huge list of acknowledged but unfixed CVEs.
Current Debian, Ubuntu, Fedora, RHEL/CentOS (EPEL) have an ntpsec package, but no ntp package. It's not used by default (that's chrony on most of the distributions), but the users can install it and use it.
It's not the issue of using the project, to my mind.
It is not even his beliefs, though many of them are — to my ears and hopefully to most — quite repugnant.
It is his attitude, approach, and at various times the kinds of people he attracts.
As it goes, I've seen him speak, back in the 90s, CatB era. He was genial enough but he seemed to have a coterie around him of rather less pleasant people. It could just have been a bad day but it has stuck in my mind ever since: it was the first time I understood that there's not really any sort of inclsive geek community.