Hi,
The Apple RAID card is the only RAID controller that allows OSX to boot from a RAID5 volume.
Yes, you can boot from a software RAID, but that only allows RAID1 mirroring.
With the Mac Pro & the Apple RAID card, you can fill all 4 bays with 500GB SATA disks and RAID5 it to give yourself 1.5TB of usable storage including booting the OS from it.
If you go any other route, you could use 1 disk for the OS, leaving 3 for a RAID5 volume. Using 3 rather than 4 disks loses a lot of usable disk space. 3 X 500GB in RAID5 only gives you 1TB of storage (as you always lose the space of 1 disk for parity).
I think you can even go up to 750GB disks, but am not 100% sure.
Simply put, if you only want RAID1, then go with software RAID. If you want RAID5 internal to the Mac Pro (as opposed to going for an external RAID enclosure) then the Apple RAID card is worth the money, as you can use all 4 drives in the Mac Pro to both boot the OS and store your stuff on.
Hope this helps!
Elliott