I would think that they don't really have a business purpose to do so since they don't sell a product and if anyone tried to sue the military over a patent the Government would just sieze the patent as being "vital to national security" or some such (I seem to recall that they can do that.)

Maybe it's a sad attempt to prove that they're on the cutting edge of technology by patenting some newfangled idea that the rest of us have been using for years? I guess they probably have some catching up to do since EDS has been "working" on their IT infrastructure for years (That's why their stock price fell by half and never recovered don't you know? Well that and lying about the revenues that were coming in from it...)

I was unaware that the US could patent anything! I thought the government had no IP rights, such as the ability to copyright or patent things. I guess I was wrong?

The US government might actually be entitled to many internet patents, as all or most of the technology behind the (early) internet was financed with U.S. tax payer money. Which, in a democratic country, should (but not necessarily does) mean that those patents are in the public domain.

isn't the US Government not allowed to have any IP rights?

IP = Intellectual Property

Actually most of the time, the government does not seize patents. Not that they don't have the ability to, or that perhaps they don't just go ahead and infringe on them sometimes, but the military spends a lot of money buying stuff from contractors/vendors every year, because the vendor has a patent on stuff. If we were in the middle of World War III, the situation might be slightly different.

So if someone in the Navy really did have a novel idea, it's not hard to imagine that they might want to get it patented, just as a defensive measure.

My big question is: if the government patents something, wouldn't the invention automatically be in the public domain, provided that it wasn't classified? Normally all products produced by government employees in the course of their jobs are in the public domain, so I would think that a patent held by the Navy would be impossible to use aggressively.

In that situation -- assuming that's true, and the Navy can't collect royalties -- then having the Navy (or other government agencies) patent stuff might be a very good idea. For the small taxpayer expense that it takes to file and maintain the patent, the country might be saved millions of dollars a year of royalties and litigation costs.

The Holy Grail when I worked with military networks (admittedly 10 years ago) was "multilevel security" which could enable a "top secret" and "secret" network to coexist and share data in a very controlled way. Information can go up, but never down. The hard part is how do you receive mail or do other things which require a two-way protocol? We built boxes which could sit in the middle and could pass messages. This appears to be a more advanced version of that.

It's a lot easier to establish prior art by pointing to a patent than in a self-maintained database. A self-maintained database of prior art that will actually hold up in court (proof of claimed dates, etc) is extremely difficult and it's actually easier to just patent something. Then you can just point to the date on your patent and no one can dispute that prior art (at least when trying to sink a patent with a later date), because those dates are maintained by a trusted and (technically) unbiased source - the USPTO.

Otherwise, you must go to extensive measures to prove that prior art document X was published on date Y.

The main reason government entities patent technology is not so they can then profit from them, but rather to give credit to the people that worked to develop that technology. Since civil servants and military personnel are not allowed to profit from inventions they create while working for the government, the patent must be owned by the organization they work for (in this case the US Navy). This prevents the civil servants/military personnel from profiting off the technology, but gives them the credit, something they can use for promotion or future job searches. To some degree this also applies to government contractors.

As a project lead for the Army at an installation that does a lot of R&D, when we patent something 1 of 3 things happen to it. 1) We grant rights to the patent to someone in industry to produce the produce on a large scale for us. 2) (more common) We just transfer the patent to the company that will produce the product for the military. Personally I think #1 is a better option, but #2 happens a lot. 3) The patent becomes public domain, and the military never has to worry about being sued over licensing issues from someone else developing the technology.

Read claim 3: "The method of claim 2, wherein the configuring includes implementing the network interface system with distinct sets of first and second processors, the first and second processors having a shared memory."
This puts the firewall smack into the hardware, not on the extension cord going out of the building. This is a firewall between computers that are in the same cabinet, not on the same internet. It also provides for loadleveling in Claim 6:
"...via an interprocessor communication channel; ...configuring the interprocessor communication channel to communicate moving averages ...and configuring the network interface system to prevent the shared memory from overflowing ...by controlling the ... network interface system. "
Further claims in the patent app show that the data is not transferred by just any program, but by an API on the firewall CPU and the boxen on either side of the firewall. This looks like some seriously secure stuff here.
Also, your normal firewall allows inside ("your" computer) to talk outside (the internet) freely, but prevents outside from getting in. This patent app specifies that the outside can talk freely to the inside, but the inside can't just blab to the world. This keeps the worms in the can. It also randomizes time signatures so that form of black box analysis won't tell you anything.