To be fair, many of the companies targeted are not exactly innocent, but many businessmen who do have valid licenses are also worried about the expense/disruption of the process. Disorganized shops who don't have their licenses nicely indexed can end up in trouble, too, if they can't manage to rummage through enough cabinets to locate copies of their licenses (one reason some have resorted to physically attaching the Windows license to each machine, so it moves with it). It's sort of like being audited by the IRS; sucks even if you weren't cheating on your taxes, except it's weird that it can happen from someone who isn't even the government!
There were also some allegations (I believe settled out of court) in the 1990s that the BSA was using its enforcement threats to coerce companies into buying site licenses of its members, because having a site license would exempt you from the possibility of an audit.
http://news.cnet.com/2008-1082_3-5065859.html?tag=lh
Interview with Sterling Ball of the Ernie Ball company.