Let's face it. If your business is built on things like web based technology (SEARCH), cloud based technology (Apps) and advertising from traffic that goes to and through your search engine or when people are looking at their content in the apps, the concept of many app stores has to be very, very scary for a few reasons.
1) Apps make the browser less relevant.
2) Apps pull subsets of data from the search engines, but with higher degrees of relevance
3) Apps keep the user engaged and away from the search engine
4) The app is on the device, not in the cloud
Most of all though the app store is all about transactions, and transactions are where Google would like to go with their Google Checkout model.
Right now, I'd say the fears are warranted as the app stores, which I think are really warehouse stores and not retail just yet, are only the tip of the iceberg of what will be the way software is retailed by brands.
We have yet to see retail marketing strategies and tactics applied to app stores. When that starts, they really will be like WalMart and 7 - Eleven.