Isn't the real problem here that instead of an honest statement about why the app needs to be downloaded (ie. no Flash on the iPad), something looking like an advertisement is served instead? That the author assumed the worst might be due to the apparent dishonesty rather than any paranoia on the author's part.
Of course, the problem might be a little more complicated, because some less adept users seeing that a website will not load on their device might blame those who made the website.
Still, CBS's solution clearly isn't the one making lemonade out of lemons.