Yes, Selenium injects its javascript into page to handle and record user interactions. It works in most cases.
For FlyTreeView control, it doesn't. So the only way to automate FlyTreeView with Selenium tests is to use FlyTreeView client-side API to expand/select/check/uncheck required nodes of treeview.
For more information on API refer to:
http://www.9rays.net/asp.net_2/treeview/miscpages/doc/ClientObjects.aspx