True. But he was using a variation of the Waffle House logo that their lawyers would argue would "confuse the average consumer", and he was using the "Waffle House" name in a domain. In something that was actually directly related to the real Waffle House. Unfortunately, their lawyers would have an easy time with that lawsuit.
If op had named it something different, and didn't use such a closely inspired logo, he probably could have kept it up. Or at least had a much stronger case of fair use. But this is always the problem with "fan appreciation" and our trademark system. In order for Waffle House to keep their trademark, they must enforce it. They cannot let a fan use/abuse it, or else it can get to the point where a judge can say it is been made generic (ex: escalator).
When I was young, I learned this lesson via a very scary letter from Warner Brothers. The lawyers aren't always trying to be dicks (though some clearly are), but they are paid to protect the brand. And someone registering a site with your brand name, putting up a logo very similar to your real logo.... is always 100% of the time going to get that C&D letter. And eventually a lawsuit if you fail to comply.