1. Many of these programs probably do not pass Apple's requirements, therefore can't be in the MAS even if the developers wanted them to be.
2. It costs $99 to submit even a free app. You need that yearly developer program membership. Freeware developers aren't making money from their programs, unless via donations. So submitting to the MAS is an unnecessary expense.
3. This point may be less relevant than the two reasons above, but the MAS is considered a ridiculous idea by some. There's plenty of reasons any "classic" user (people who prefer the "old" way of doing things) can find to dislike the MAS. One is that you can't submit installers (to my knowledge), and you can only submit standalone apps. Another is that apps are restricted, probably the worst part. And another, that you have to pay even for submitting a free app.
I personally prefer installing things the "old fashioned way" as opposed to the MAS. Whenever something is on the MAS that I want I look around on Google and the developer's website to see if I can download it anywhere else. When I can't find a web download version I get quite annoyed. If you ask me, the MAS is a bad version of what should've been a package manager. Anyone who's used a Linux distro may know what I'm talking about. Cydia is a package manager too, for those of you who have jailbroken iPhones.
Package managers are freedom. They simply download a package, and install it according to how it was put together. You can add repositories that have packages you want, and anyone can start their own repository. There's no approval process and nobody to make arbitrary decisions as to whether or not your package is allowed. And packages can work just like installers do. Package managers have no walls, no boundaries. They put the user in control.
Now the MAS, is a walled garden. Things may be nice and pretty inside the garden. You may have some good things inside the garden. But the fact is, there are walls, there are restrictions. You can't get anything outside the boundaries of the garden. You don't control it. If Apple doesn't approve of your app, they don't let it into their garden. It is the opposite of freedom.
For this reason alone, I would not want to put any program I plan to develop on the MAS. I'd rather release it on a website. Plus, what if I need an installer? What if I need to set certain files in place before the app runs as they are required by it? Well too bad, Apple seems to hate installers for some reason.
As I said, walled garden.
/endrant.
Anyways, as I said, reasons 1 and 2 are probably the most relevant. Although developers who have a philosophy of sorts when it comes to things like this, like I do, that may be their only reason for not using the MAS.
