The main benefit of a Windows Server is having a kind of known environment you work in. Also if you want to use more Windows specific features like Active Directory a Windows server could be handy.
But! you have licensing cost and are bound to Microsofts update, release and lifetime policies.
Using freenas or a similar system has advantages. No licence fees, huge communities and a huge softwarepool which is easy to use and install.
Using freenas or anything else which uses zfs as a backend storage is a great choice btw. ZFS offers a lot of features Windows filesystems don't(as far as I know) and is able to detect data corruption a normal raid cannot, due to checksums for each block stored on the disks. Disk failure is not a binary thing. Data on your disks may get corrupted while the disks reports no error and the datablock gets read perfectly fine....