I think it's more about seething hatred for Microsoft than it is about logos. I mean... no one seems to mind IBM logos (hell, we even distinguish rarity based on the color).
I think what's on our keyboards gets shifted into ultra picky mode when it can interfere with the layout. A lot of boards also have been around before a keyboard even had a "windows" key, so it could be the purists in all of us.
Honestly speaking, I use it for numerous features, (Run, Lock, Search, Win+pause/brk for easy access to "System"). On top of that, I try to use my mouse as little as possible. Something like Windows and then down arrow opens up my web browser.
It's a shame how it steals focus though...I think a big draw back and a lot of hatred comes from gamers. Easily avoidable with something like AHK or KeyTweak but still, a very sh*tty button in terms of it minimizing a full screen game and stealing focus.
As for the OP, I don't really think "Alphabetical" is the best way to have access to most commonly used keys. If you take popular fast layouts like Dvorak and Colemak, they put commonly used letters right where your fingers should be resting. Which makes more sense to me. Also did they brand the name of it "New Standard Keyboard" in hopes that that would catch on? "Well it's called new standard...it must be the new standard".