Yes, the protocol your computer use across the network is independent of your file system type. That's why you can trade files over the Internet and to a Linux machine or a Mac OS.
It's just when you're transferring file from hard drive to hard drive in the OS, if your on Linux, chances are by default your running reisfer or ext3 and Linux doesn't support NTFS write by default so you can't do that unless you compile your kernel for NTFS write support. That's one example.
Or when Windows canÂ’t see Linux file system type, another example when you dual boot.