We can duly expect most ads (though possibly not all) to be genre-related, or targeted at the readers that are assumed to read that genre. If the ads are properly targeted, the reader will not feel "intruded upon," because the ad will be for something they most likely have an appreciation for. As these are the more likely people to respond to an ad with sales, this is what the advertisers will be aiming for.
Hence, e-book ads in most cases should be well-targeted and unobtrusive, even desired (or at least looked forward to), as kjk describes. Any advertiser that breaks this obvious rule would be stupid, because it would only annoy potential customers and lose sales.
Advertisers can rarely afford scatter-shot advertisements in isolated locations... it's bad business. To expect them to put scatter-shot ads in e-books would make little business sense... they'd be better off putting their ads on a subway car.