This is a good question to ask for sure. The main reason is one of software design choice. FME Server could have been engineered as a single, multi-threaded application and then you would only see one process. The potential problem with this approach is if a thread crashes, then the entire process crashes. We choose to separate each functional area into it's own process to avoid this and provide better fault tolerance. Google's Chrome browser does the same thing, where each tab is a separate process.