Scalping is simple, capitalistic, Marketing 101 of supply & demand. As long as people are willing to spend x number of $ to see a performer at a venue that can not accomodate everyone wanting to see said perfromer, there will always be a shortage of tickets and a premium placed on the tickets that ARE available. Of course with the robo buyers mentioned above, this further reduces the lot of tickets available to the general public.
I have been going to concerts for a long time and it appears to me that even the promoters and venue themselves often times 'hold' back a certain number of tickets, and I wouldn't put it past some of them that they are also participating/inside source, etc. of working with these robo buyers. When you think about it, how many of us have ever gotten tickets in "pre-sell" that were really good seats in the lower levels, on the floor, first couple of rows, etc. Why? Because often times these seats are still held back by the promoters or not put into the general pool of tickets for available to the public.
Honestly, I wish the bands could just sell all of the tickets themselves, but the promoters, venues, etc. will not let them. In the case of Phish though, it would be nice if the band would/could negotiate with these venues & promoters for the rights to sell at least 50% of the tickets through their own system to eliminate(as best they can) that the majority of tickets go to their true fans.