Specifically in the case of Hey:
* Bandwidth to deliver the app to each user that downloads it
* App Store Review requires human beings, so there's paying those people
* There's also generally maintenance of the App Store servers, backend software, etc.
In the past, I'm sure Basecamp (the app) was featured somewhere on the App Store and thus got featured and brought more eyeballs to the app. These features are done by actual people and there's a cost there.
Any store has a cost. Lets say Basecamp were to be able to side load. Now they'd have:
* Bandwidth for delivery of the app for each download
* Cost to maintain their servers
* They'd have to maintain whatever delivery system they had to write in order to provide the same features of the App Store
* They'd have more support costs as well because can the average person understand side loading? What happens when that goes wonky? Now it's on their support team to handle that business too.
Apple provides a lot of value there.
Edit: Jesus... I hate the formatting options on this site..