According to their blog, jQuery Mobile's version 1.1 will greatly enhance the "fixed" toolbar issue. If you use it now, you'll notice that the header and footer toolbars aren't actually "fixed" as you would expect. Instead, they scroll with the page, and then are dynamically re-positioned.
"the way mobile browsers would freeze the DOM during scroll would result in the toolbars briefly scrolling with the document which was impossible to completely fix" – jQuery Mobile Blog
jQuery Mobile says they have completely re-written the plugin from scratch to fix this issue.
Although, if you notice, form fields show up OVER the toolbars in the demo. Hope they're fixing that!