No, there just has to be a risk that consumers think that this is somehow associated with Waffle House. The point of a trademark isn't directly commercial. It isn't about preventing other people from making money from your brand. It is about protecting the integrity of your trademark so that when users see your name and logo they know it comes from you.
Basically trademarks are like a signature, they "prove" who you are doing business with.
> there just has to be a risk that consumers think that this is somehow associated with Waffle House
More than risk; some of the tweets could be actual evidence of that confusion.
I think if the general branding vibe of the site was more about hurricanes and only made a reference to the "Waffle House index" via NOAA, it might have had better chances of surviving. And also a big disclaimer that there is no affiliation with WH would have also helped.