This happens because most sites are still optimized for desktop use, with little or no testing on iPad. You'd be amazed how broken layout or JS on vast majority of websites are, but few mention this because modern browsers do a decent job of working around say, JS bugs. IE is especially good in this respect. So people test their site on say, IE, Firefox and Chrome, and fix bugs until it works fine there, not mentioning a lot of bugs they still left which were worked around by the browsers, then you open it on your iPad on which they didn't test -> epic fail. Which doesn't say anything bad about iPad's hardware or software really.