You should read it again; there's a 4-hour "maintenance window" every week where any required changes will be applied, but downtime is limited to the time necessary to apply the changes, not the entire four hours. And you can select the 4-hour window that's most convenient for you.

For larger sites, this seems like it would hardly be a problem...if you have a pool of RDS instances, you could just stagger the maintenance windows so you never have more than 1 of your instances down at a time.