Well, a couple of reasons:
1. Apple is not running a religion, they are running a business(a fact that may be hard for open source true believers to understand. If you value ideological purity above all else then I guess its natural to assume that everyone around them must be doing the same thing). At the end of the day, Apple?s business tactics must serve their bottom line (not the other way around). Apple may have a product design philosophy that helps them achieve their business goals, but if it comes down to a choice between philosophy and money, money will always win (bringing back buttons on Shuffle, etc). Throwing away giant sections of the professional market by forcing all software to be sold through the app store is not in the financial best interest of the company. Professional software vendors like Autodesk, Adobe, Ableton, Wolfram, etc are hardly going to let Apple take a 30% cut of software they sell for thousands of dollars. There is no high end professional software market for iOS. There may be one someday as different device sizes proliferate and Apple may re-evaluate its position as a result. But for now, iOS is primarily to serve consumers.
2. OSX is a workhorse that has to satisfy a variety of markets both technical and non-technical (graphics professionals, architects, musicians, scientists, educators, students, moms and grandfathers). It has to be many things to many people. Some of those people would probably love for an even simpler computing experience (moms and grandfathers). Not making an easy, simplified appl purchasing and installing experience for these people is tantamount to leaving money on the table. It?s also leaving money on the table to not make a way for small developers to put their software in front of an unprecedented number of eyeballs. iOS is much more focused. Ease of use is paramount. And Apple is still growing a market (the app store) that didn?t even exist 30 months ago so they probably aren?t don;t have too much time to worry about about growing a professional software market just yet. Again this may change one day as smartphones mature and form mobile OS?s come in a variety of form factors, but for now this is the experience Apple is selling.
The fact that you think Apple users will ?do as they are told? shows that you have disdain for people who choose differently than you. That is too bad. There is plenty of room in the marketplace for different approaches to computing.