To be honest, here are a few reasons:
1. The many times I have been to the local Apple Store, I have never seen one Mac Pro sold, EVER.
You must have only have the 'mini-store-for-retail-mall' store. The full size stores typically have one on display. The only time it may disappear from stores is Holidays sales seasons when stores are overstocked with product and they use part of the display space to hold smaller, more faster selliing products so people can "buy and go" in order to keep the lines shorter inside the store.
I've been to 10 different Apple stores in 5 different cities and have only seen the Mac Pro missing from the smaller mini-store. Pretty sure Apple is in process of dumping those mini-stores where it can (leaving the mini or micro stores to the BestBuys and Targets ) so it is long term it isn't a issue.
Furthermore, the physical stores are not decisive for Mac sales. On the last conference call Apple reported they sold 5.2M Macs. The retail stores sold 1.1M Macs. That is only 21% of Macs sold. I'm not sure why anyone would want to go to the local "let's go hang out with Biff and Buffy" retail mall to buy a Mac Pro anyway. Some Pro Camera equipment shops sell Mac Pros and much less of the Apple product catalog. Apple even has a page to find other specialized resellers.
http://www.apple.com/buy/
2. Apple doesn't seem to be putting much emphasis on the Mac Pro with marketing,
This is an exceedingly dubious point. There are no Mac ads right now period. This has nothing to do with the Mac Pro.
Apple did this with the first Mac, the 128k, it was their $2499 Power machine, now they sell a $2499 Mac Pro and don't market it ANYWHERE?
And yet Mac sales are up year over year despite the TV campaign ended over a year ago. The effectiveness of TV is overblown. Apple blew alot of money on Mac ads, but that not necessarily what made them successful but then and now.
3. Apple is focused on Portables / iOS / iPhone / iPad right now.
That's because consumers are
buying them and they show high growth. In the Mac portion of the conference call Apple something to the effect of "MacBook Pro and MacBook Air = VERY strong growth ". People keep hand waving doom and gloom about profits and focus. It is not the metric that Apple is closely watching or using to adjust spend.
4. Go to an Apple Store and say you are looking for a powerful desktop, they will point you to a 27" iMac, not a Mac Pro, they will even try to talk you DOWN or OUT of a Mac Pro and say you DON'T need it unless you are a film editor or run a studio.
Apple store sales folks are
not suppose to upsell customers. They are suppose to ask questions and guide the customers to computers that meet their needs. If a better match means guiding a customer to a lower cost Mac that is what they are suppose to do.
Generally speaking the 27" iMac is an powerful desktop. And frankly a statement of "I need a powerful computer" is so vague as not warrant the additional spend for a Mac Pro. It wasn't wrong to recenter the discussion around the middle ground Mac desktop offering and see if follow up questions pointed back to the Mac Pro.
The "don't need it unless you are film or studio" part is silly. My impression this is as much a part of the cultist Mac kool-aid folks propagate as much as specific Apple training. I've heard goofy things like "Macs don't get viruses" from Apple geniuses too.
To be fair though many people will come into the store talking "powerful" when what they really mean is not computational power it is more "control". If state "I want and box I can open and rummaging around on the inside" the Apple Store sales person probably would let you easily slide over to the Mac Pro. That is in contrast to "the data working set for my software seems to require more than 16MB of RAM which Mac should I buy".
5. Like I said before, Apple killed XServe, they butchered the new FCP, they will do the same to the Mac Pro. The Mac Pro's days are numbered, it will be discontinued as Apple sees their profits coming in from all other sectors.
It is not about profits. It is about growth. The Mac Pro has to roughly track the growth of the other
Mac products. The other Apple product areas are immaterial.
Mac Pro is not selling well, it is the lowest on the totem pole as far as sales go --
It wasn't all that long ago when the MacBook Air was the lowest selling product in the online Apple Store. (the Mac Pro outselling it despite being almost twice as expensive). Apple "fixed it" and not it is selling in higher numbers. Same with Apple TV results in last conference call. Last fiscal year Apple sold 2.8M units. This just completed quarter 1.4M units. One quarter as many as about half of a whole previous year.
The core point here is that Apple is patient. Even more so now that they have a huge cash hoard to be patient with. If they see a long term path to something better they will take it even if there might be hiccups in the short run. The component supply for the Mac Pro has been having some hiccups over the last couple years ( incomplete Xeon 3500 updates , multi quarter slide deliver dates ).
With new Xeon E5 updates and PCI-e v3.0 graphics/GPGPU cards and new software that can better leverage parallel and heterogeneous computing, there is plenty that can be utilized to "fix" the Mac Pro and put it back on a growth curve.
Apple could also drop a Mac Pro in the $2,000-2,500 range which would also help "fix it". The average selling price right now is a bit too high. They need a broader range of product that isn't a price overlap threat to the iMac.
Money -- the bottom line at Apple right now.
Again go back and watch the Steve Jobs video. To some extent Apple treats money as a by product of consumers voting "thumbs up" and buying the product. If consumers walk away from the Mac Pro then yeah sure... they'll cancel it. But it is not a zero sum game contest between Mac Pros and iPads/iPhones. If people continue to buy more of both they will make both.