What about the overhead of the POSIX emulation layer? From a non-cygwin-hacker's point of view, every cygwin app I use seems slow relative to its equivalent windows port, though I have no metrics to back that up.
Besides, with cygwin, you're requiring UNIX sysadmin knowledge to some extent (watered down, yes), even though the host OS is NT. I don't know any dyed-in-the-wool NT people who would look forward to supporting a pseudo UNIX environment, so the converts would be few from this approach. It's likely, though, that the command line-driven, config file-editing nature of AOLServer would have filtered out that crowd already. The question remains, however: If the admin is comfortable supporting a UNIX emulation (that possibly has bugs itself) on top of a Microsoft OS (which possibly has its own bugs pertaining to cygwin's lower-level interfaces), why would the same admin not be comfortable installing RedHat? Of course, I suppose there are a bunch of potential beurocratic/corporate reasons, in addition to a very rational fear of the learning curve of Linux sysadmin, but I frankly question whether a windows-only shop would really consider running OpenACS on top of an emulation layer.
Of course, as a development platform for the window-phile hackers out there, cygwin would be great. Who doesn't get a little thrill out of running a fully operational db-backed web site off of their laptop? :)
