Sandboxing is a preemptive protection from as-yet-undiscovered threats.
It used to be that the operating system was the most common attack surface for any computer. Malware writers looked for operating system flaws in order to spread malware.
However, these days, operating systems--even from Microsoft--are pretty robust and are becoming difficult targets. Mac OS X has always been a very hard nut to crack, and with Microsoft getting serious about security, Windows flaws are becoming harder and harder to exploit. So these days, the majority of malware is spread not through operating system flaws, but through application flaws, with Adobe Acrobat Reader being a great example of a seriously flawed application that's prone to attack.
The idea behind sandboxing is that if a flaw exists in an application that allows a hacker to create a document that will exploit the flaw and allow the hacker to execute arbitrary code, the hacker is still limited in what he can do. An app exists inside a "sandbox"--an enforced perimeter that the operating system provides. If an application attempts to do something that violates that perimeter, say by accessing the system files on the computer, the operating system terminates it.
In a world where most malware is spread by infected documents that corrupt the application that is used to read the documents, sandboxing is very important. It is reasonable for Apple to require software they distribute to be sandboxed.
A lot of folks believe that Apple will soon forbid distributing software except through the Mac app store. I find this belief to be deluded. It ignores reality--OS X isn't a locked operating system; few people would use it if it were; large, complex apps like Adobe Creative Studio are unlikely ever to be distributed via the MAS; developers would be unlikely to code apps for such a platform...
The delusion comes from the fact that people look at smartphones and think of them as portable computers, and so ask "Well, if smartphones can be locked down, why can't computers?" But people use smartphones differently from computers and have different expectations.
A better analogy is to think of smartphones like video game consoles. Ever since the first Nintendo, game consoles have always been locked. Console makers tightly control the market for console games, they must approve all games, they charge developers very high fees to develop games (when the PlayStation came out, game developers had to pay more than $10,000 to license the game development kit), and the console makers always get a cut of every sale.
The Sony PlayStation line of consoles is far more tightly locked down than, say, an iPhone, but nobody says "See? This means Sony is going to start locking its VAIO computers too!" because we don't think of laptops and consoles as similar, whereas we do think of laptops and smartphones as similar. But the way we use them is still very different, and trying to lop a desktop operating system makes it far less useful. Apple is many things, but it's not stupid.
