My iPad is new (1 month old). OS is 4.3.5. Safari is as-delivered.
There are explicit directions on post #13 on this thread on how to reproduce the ocw.MIT.edu video problem.
If there is now some sort of Flash bypass on that site, my straightforward entry to these courses must be bypassing it. Ergo, a small bug needs to be fixed on the website.
However, Apple's Flash ban is the real source of a much larger problem, which impacts many online courses at many universities. Negotiate a Flash license ASAP, Apple.