Imagine if your app made $30,000 in the first month it launched. That's great, apart from the fact that you have to give Apple $9,000 of that. Is the service they provide really worth that much? I'm not so sure it is.
My little company wouldn't be able to survive if I had to give 30% of my revenue to Apple. While I hope to change that, Click On Tyler simply doesn't operate at a scale where that's sustainable.
Ember for Mac was in four different bundles in the last half of 2014. It earned an extra $80,000 (USD) in revenue, not only that it also brought in a lot of new users. If Ember was only available in the Mac App Store I wouldn't have been able to do this and Realmac would have been worse off because of it.
I've participated in a few different bundles over the years. And, while they have brought in a nice bonus bit of revenue, I've found the ability to market to that huge base of new customers more useful.
Here's the biggest and most important difference of all, by selling directly you get to know every single one of your customers. When building a business your customers are your most valuable asset, but yet when you sell on the Mac App Store you don't know who they are.
Bingo. Over the years selling my apps I've formed many great, personal relationships with my customers. They've become key advisors when I experiment with new product features and services. They're also a constant stream of ideas and improvements that I wouldn't normally see since I'm so close to my apps. Customers on the Mac App Store rarely translate into this kind of usefulness - if you even know them at all.
All that said, one distinction worth making is that Dan doesn't advocate not selling through the Mac App Store. He simply says that you shouldn't limit yourself to only one sales channel.