The founder of an open source project he founded should step down because you don't like his opinions? He's allowed to be pissed off that some other company is profiting without contributing back. Developing the single most popular website framework is not without cost. Don't like his paid service? Don't use it!
Reading Matt's post, it's not my impression that he's really pissed about that – that seems more like an additional (less important) aside.
His core complaint is, paraphrased, "WP-Engine offers WordPress hosting, but all they offer is a bowdlerized version of it, which reflects badly on all of WordPress. So I'm pissed about it because I spent a lot of time and money on WordPress and I care about it a lot".
This sort of thing comes up every now and then in different contexts. A few months ago the Debian developer decided to offer a bowdlerized version of KeepPassX and was then excessively abrasive and rude about it when people complained. At the core, this is the same kind of disagreement/conflict.
All of that only amplifies your "he's allowed to be pissed". I'd probably be slightly more careful in my use of language, but I'd be pretty cross too.
Certainly doesn't seem like a resigning issue. The hell is up with that?