They are not using any queries that are not supported on mysql 4.1 and for myisam use, 4.1 is faster than all later versions of mysql until version 5.5 (which is not available yet on many control panel based servers like cpanel).
The decision not to change any queries was made early on, 3.3 will bring a few query changes, There are queries which have been wanting MySQL 5 optimizations for awhile now, ultimately, this is going to bring performance improvements to (currently) 98%+ of users, with the remaining 2% likely to never update to 3.2+ or (based on your statement that 5 is slower than 4.1) slightly slower performance than previously,
Also, The WordPress stats[1] indicate that 2.7% of installs were on MySQL 4.1 (with 0.2% on 4.0, which was last supported on WordPress 2.8) - MySQL 4.1.2 has been required since WordPress 2.9.
Genuinely glad to hear that WP has this foresight in their roadmap.
By declaring right out that it is no longer going to be supported, people will be encouraged to write for the newer databases. Eventually when the standard MySQL version moves up, it won't be stuck in 4.1. Plugins authors will also appreciate that they have been given enough heads-up to update their plugins.
This will also give people time to upgrade their databases if they're managing their own.
And there's your problem.
Of course, if someone is using WordPress at all in a low-end virtual machine, then you could also point at that and go "And there's your problem." With some justification.