The differences between Falsh and and HTML5 videos is on the site you access, not the iPad or Safari, so if a video is only in flash format on the site, no, Safari will not be able to play it. More and more sites postiong video content are moving from Flash to HTML5 based video display, but certainly not all.
Possible options, depending on the source of (site containing) the video:
- There are several apps (braoswers) in teh app store that route the flash content to a thrid party server, convert it and send it back to your iPad. Reveiws and results are mixed, so you will want to read the descriptions adn reviews carefully. iSwifter seems to be popular. I have no experience with any of them.
- Many sites have accompanying apps in the app store.
- Check for an alternative source. YouTube's mobile site actually works very well with Safari these days.
- Give up and access the site from a computer.