Oh yeah, it'll work in a windows environment.
You're doing a web app, right? So all that means is that your webserver will need the Java runtime installed on it, and your project needs the FOP files included (well, we include them anyway). The FOP can be called direclty without having to have any interface load up or anything (in a way, its almost like you're using just another class, except you have to do a shell command to access it).
If this isn't on a webserver, then you could still do the same thing...but it would mean that each user would need to have the FOP and the java runtime installed on their machine. It actually might be easier in this case to implement it as a webservice, which takes an xml document and converts it on the server, displaying the pdf in a browser.
hth
D'Arcy