Why are some graduate schools' students so much more productive?
The "fundamental difference" that you talk about should arise in three things:


The fact that a student made into the top 5-10 schools implies (not perfectly, of course) that the student has acquired a good amount of knowledge in the field and that he or she works very hard. This means the filtering, and thus a difference arises even before the program could start. It's not hard to assume that someone who gets into a top 10 school has worked harder in life to get there (of course, there are always exceptions). Thus, such a student is bound to be more ambitious, and would not settle for that one thesis at the end of their course. 
Even if you're not that ambitious, seeing many peers around you publishing papers may encourage you or add pressure to do exactly the same. In life, we often try to rise up to the standards around us. If you're in a less reputed college with less motivated peers, you might be satisfied with good grades and a thesis. But if you're walking amongst other motivated people, you'd soon feel lesser and try to get on par. 
Good schools attract good faculty. It's much easier to write a research paper and publish it with the guidance of a great professor. 


We can see that the two principal differences arises without any effort on part of the college or university at all and solely because of the peer group. And that's an important factor in academia as much as it is in the real world.