The iPad version uses Quicktime instead of Flash. Obviously the iWhatevers don't support Flash (which is one of the few things I respect Steve Jobs for). Flash support outside of Windows is awful, and not that good on Windows either.

Anyway, I sent an email to the BBC complaints department a few weeks back saying that the BBC oughtn't rely on Flash for their iPlayer precisely for reasons of poor support outside of Windows, and if they can Quicktime versions for the iWhatevers, then why can't other devices access those encodings.

Their response was:

"We can't commit at this time to which devices we will make available but we are
working on other ways to make BBC iPlayer available. It is our aim to make it
available on as many platforms as possible.

Nevertheless, I can assure that I have fully registered your comments on this issue. They have been made available to those responsible for maintaining the BBC iPlayer service."

Which is a bit of a brush-off, but at least it adds another voice to the dissent.
I would suggest that other people also send a complaint to the BBC stating that they can't access the iPlayer stuff on their N900 (or whichever device). The more people that make it an issue, the more likely they are to consider more open standards.
https://www.bbc.co.uk/complaints/forms/