From my perspective the main things that killed it were online shopping, as the article mentions, and computing just becoming more boring, at least from a hardware perspective. Once the iPhone came out, that became many people's primary computing device or computing peripheral. Everything you needed was just an app or software which you could download online. The great mass of consumers just need a laptop and a few commodity peripherals, and they can get all that at Walmart. Then Newegg came along and really ate the PC hobbyist market.
Eventually Fry's succumbed to the GameStop effect - their primary market is completely eaten out by online competition, so they fill their retail space with cheap garbage to make ends meet. The last few times I visited my local Fry's it was more empty shelves and cheap bargain bins than anything I was interested in buying.
It was a sad end, but not surprising. I just don't think you can justify having large specialty stores anymore when online shopping is so convenient and the options are so much more plentiful.