It may seem counter-intuitive, but the answer is Apple.
Apple tightly controls what apps make it to the App Store via its approval process. This process is designed to ensure that apps at the App Store meet Apple's content guidelines (these get applied unevenly, but have to do with violence, adult content, and copyright infringement), don't compete with Apple's own apps, and that they have good quality code and aren't malicious (this doesn't work perfectly, either).
As a consequence of this system, though, many apps get rejected. Some of these apps are perfectly good and useful, but run afoul of Apple in various ways, especially by competing with Apple's own apps or by allowing users to do things with their iOS devices that Apple doesn't want them to.
That's where alternative app stores like Cydia and Installer.app/AppTapp come in. Since these stores aren't part of Apple, they have different rules (and don't have Apple's strict approval process, either) and can offer useful apps that Apple won't allow at the official App Store.
Though installing apps that aren't checked by Apple (and on jailbroken devices) may have some risk, these alternate app stores provide a useful space for edgy apps - assuming you're willing to experiment with them.
Got a tech support question? Ask it in the discussion forums.
Want tips like this delivered to your inbox every week? Subscribe to the free weekly iPhone/iPod email newsletter.