While I woudn't use it, heck even Windows is used in many factory automation environments and believe it or not
is used inside many ATM machines.
Many of that is driven by total deployment cost associated with Windows-based solutions: they are easier to develop, easier to document, easier to certify, and easier to upgrade, than a naked solution on a mcu based solution.
Netduino, Pi and other "big" micros can potentially develop into a whole market where a simplified version of OS (Linux, windows, etc.) can run with the sole purpose of providing an abstract layer to "hide away" the hardware so to lower software costs across multiple platforms.