In my personal opinion, FreeBSD is better, at least for the "appliance" I run at home. Reasons: Much more manageable OS (not so much bloat, version changes are under control), not controlled by fundamentally one company (face it, the Linux ecosystem is dominated by RedHat), more stable ZFS implementation. Actually, I think OpenBSD would be even more suitable, except that it doesn't have ZFS (requiring the use of a separate RAID layer, big management headache), and that it is even further behind on driver support (to the point that using OpenBSD as a wireless AP is virtually impossible, or at least it was when I switched to FreeBSD).
But then, my "appliance" at home is nothing like the style of appliances that Netapp, Isilon, and Panasas sell. It is neither appliancified (it gets managed by logging in as root and issuing commands, with lots of reading of man pages), nor is it of the scale of these systems.
In reality, the companies you mention don't just "use" FreeBSD. For example, if you were to take a NetApp, and decide to upgrade FreeBSD to release 10, it would completely stop working. I don't know exactly which FreeBSD version NetApp's software is based on, but I'm quite sure that it is (a) very old, and (b) considerably modified. That is one of the advantages of *BSD over Linux: You can modify the source, and ship the resulting system to your customers, without running into GPL hell. Matter-of-fact, I'm quite sure that one of the major reasons for companies to use *BSD as a base is to avoid GPL hell, and the lawsuits and copyright compliance costs that come with it.
On the other hand, Linux has lots of advantages too. The biggest two are: (a) Driver support, of the highest quality and the best vendor support, for up-to-date and high-end hardware. If you call Mellanox or QLogic or LSI or PMC-Sierra and complain about a bug in their device driver in *BSD (or HP-UX or Solaris or AIX or another boutique OS), you may or you may not get help, depending on how much financial clout you have. If you do the same for Linux, the bug is either already fixed, or they will jump to it. (b) Stability and performance, in particular for very large systems. I've seen Linux run on systems that are completely outside the scope of amateurs (and much larger and faster than the building blocks that Isilon or Panasas use), systems whose cost is in the range 10^5 to 10^8 dollars, and with Linux it's usually flawless: Boot from a RHEL or SLES image, and an hour later you have full function and great performance, with little tweaking or tuning required.
The reality is that there are also quite a few vendors that sell storage appliances based on Linux. Interestingly, there are still vendors selling Windows as a storage server, and they're making good money with that too.
If you are looking for vendors that use ZFS as a storage appliance, there are examples too. OSNexus comes to mind (they're using ZFS on top of Linux). There are examples of companies that sell storage appliances based on Linux file systems (although I know of no single example that uses BTRfs, which seems to be considered a data-losing machine, nor ReiserFS, which has serious problems, in particular for the wife).
P.S. (I'm editing this post): Just because I point out some disadvantages of *BSD and advantages of Linux doesn't mean that I'm trying to imply that Linux is the better choice for a storage server or appliance. Rather on the contrary. If I were chief architect at one of Isilon, Panasas or NetApp's competitors, I would recommend using FreeBSD as the base operating system. In reality, engineering is the art of the compromise, and various operating system bases have advantages and disadvantages. I'm just correcting the rather black and white exaggeration of the original post.
