Nios II flash programmer error

From the numbers it seems that nothing is constrained. Are you sure this is coming from a kit example design? Isn't there a sdc file you can import with the input/output constraints?

What does it say in the "clocks" tab in the report? Do you see all your clocks at the correct frequencies?

If you need to set up your own constraints, you can start reading the timequest user guide (http://www.alterawiki.com/wiki/timequest_user_guide) to understand how it works.