Through history and marketing, Cisco has established themselves as the "name brand" in the market. This naturally means they can get away with charging a hefty price premium for that name, and they'd be less than capitalists if they didn't take advantage of that. Cisco's competitors have to price their products below Cisco because of this positioning. Also, Cisco sells to business customers, who tend to be less price sensitive and more reliability/support/feature sensitive than SOHO customers. If I save $1000 on a router and it dies and my company's offline for a week, I didn't really get a good deal.
Cisco's fat margins do give them broad ability to discount when they need to. They aren't stupid about their cost of goods, though they do still have a fundamentally higher cost structure than many of the Taiwanese/Chinese low-end manufacturers. But Cisco's list prices are a polite fiction, like much of the business oriented IT equipment pricing. Everbody gets a discount, it's just part of the sales game.
Is Cisco gear higher quality than Netgear? Hmm. Not such a simple question. On average, I would say yes, slightly. But both manufacturers have had some products with bad records, and both have had some products that were incredibly solid. I think what you're buying and how you use it (proper environment) will make a bigger difference. Feature wise, a real IOS Cisco box probably trumps Netgear with ease - Cisco's got a LOT of enterprise features.
All that said, the Cisco acquisition of Linksys is incredibly interesting because it is a move into the SOHO low-cost / high-volume space, somewhere Cisco normally just doesn't play. In that game, price is very important (would anyone buy a Linksys SOHO router if it were an order of magnitude more expensive?), and features/quality get traded away for that. And at some level, Linksys competes with low-end Cisco quite successfully, so Cisco is cannabalizing their own low end line.