The way I view it is this: doujin is a hobby, not a job, or at least for most of the individuals involved. Just as /u/Callinectes mentioned, all of us, including the doujinka, don't want to just inconveniently give up the hobby. They too are just looking to have fun like we are by contributing to the series we know and love. It just so happens that the original creator or the related publishing authorities want to maintain intellectual property rights. To some degree this is definitely OK, but more often than not, if they see doujins being mass distributed on the net through piracy, they'll assume the doujinka is at fault for mass distributing derivative work that may be impacting their profits. ZUN isn't one to do so, but many a doujinka have had this issue with other series. In the case of Touhou, if a doujin work superceeds the distribution scale of the original games, ZUN's trademark over the series comes into question, and in fact there was indeed a commercial group that tried to wrest the Touhou trademark from Team Shanghai Alice at one point (let me see if I can find the article on it). Like I said before: a few little shits ruin it for everyone.

While I do agree with you that the inability to distribute over much more open channels is pretty retarded, I believe it is not without good reason. ZUN doesn't want to lose copyright. We don't want him to stop making official Touhou goods. The dojinka doesn't want to stop making doujins. ZUN doesn't want to stop them, or doesn't care too much so long as it isn't bothering his works. We don't want either of them going kaput, but the need for control over distribution is definitely real.