The culture of any community is shaped by the worst behaviour that is tolerated. Related: Why unmoderated online forums always degenerate into fascism https://www.salon.com/2019/08/05/why-unmoderated-online-foru...
No, the phenomenon that lasted really only a few years was due to the fact that the first Diasporas kicked off of those sites (or that left due to crack downs on their expression) were existing hateful communities. There's a name for the effect that I can't quite remember, but basically new communities are unsavory at first because they're made up of the unsavory characters that are unwelcome at the other communities, and this prevents their growth.
Thankfully we are currently seeing that effect wind down as well. With the increase in moderation beyond plainly hateful content, now to anything a site deems unlikeable, you're seeing those Diasporas become less and less unsavory and more mainstream sets of ideas are being discussed on the newer forums.
I regard articles like the one you linked as yellow journalism, designed to discredit people's desire to collect and discuss ideas online, freely, and argue in favor of places where ideas cannot be discussed freely. If there is any one thing that causes sites to become hateful, it is the need for the site to promote "engaging" content for as profit, something you are less likely to see on newer sites with less commercial pressure.