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Several sites, including YouTube, offer an HTML5 alternative for devices that don't support Flash. YouTube has been accessible by iOS devices since the beginning, or close to it, by the stand-alone app. The support has not been, in my experience, comprehensive, and I believe that some videos have a non-Flash version stored that works pretty seamlessly and some do not, but attempt an on-the-fly conversion, which works less well and sometimes fails. Or at least that's been my experience.
The fact that iPod/iPhone/iPad had a functional YouTube app shows that YouTube has had the ability to offer videos in a non-flash format, but it is relatively recently, I think, that they have recoded their site so that you can access those videos without going through the app.
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