Quite aside from developing apps - or webapps, iPads are accounting for a significant and growing proportion of traffic to websites through the browser. To optimize a site for both PC web and for tablets, there's certainly more to it than just offering alternatives to Flash.
For example, 'clickable' areas should be defined as larger than normal, text size should be reviewed; sites should define input fields as e.g. 'search' or 'email address' so that the appropriate keyboard displays on the device.
Very interesting topic. In the usability field, we know that there's no "one size fits all" UI when it comes to the various input modes. That is, designers must take into consideration the prevalent input mode (e.g., touch on a tablet) when designing a software UI. Of course, they can take the "lowest common demoninator approach" (for example, creating targets that are large enough for touch but are still usable with more traditional means of input, like a mouse & KB). However, there is almost always a human performance hit that comes with doing this.