Part of the reason for the difference is that The Guardian on-line audience is larger and generally more engaged than that of The Times. Part of this is because The Guardian have been very forward thinking by newspaper standards in their use of the web, but it's also because they have a younger more technology aware audience than The Times which tends to be older. There are ways of addressing this (for instance The Daily Mail on-line is a very different beast to it's paper version with a very different audience - one all pictures of pretty ladies in short skirts, the other righteous indignation at such moral outrages as pretty ladies in short skirts) but it's core following was always going to be harder to convert.
Also remember that subscription doesn't mean zero ad revenue. The Financial Times gets just under £30m a year from advertising on-line despite being a subscription only service. Part of that is down to the fact that they appeal to a very specific, target-able demographic but that would also be true of The Times to a lesser degree.
All of this doesn't make what The Times has done right or wrong, I'm just saying it's not as cut and dried as Rory Cellan-Jones implies. It's early days for The Times and I wouldn't write it off quite yet.
P.S. The iPad app is still a subscription as are the Kindle downloads. They're all revenue for the electronic content so I think it's fair to count it.