Agreed! I wrote a blog post about this a couple years back.[1] A few things I think are going on:
- layout and hyphenation algorithms on the web are worse (or often disabled!)
- the lines are often too long
- the site's margins aren't as strong as with print design
These factors combine to produce the mess you're describing.
I've spent so much time reading justified text in print that I do like it in general. But I think until places like NYT or Medium adopt it on their websites, it's probably not up to snuff on the web.
(edit: formatting)