That all sounds rather strange. Have you created that file using the very same yEd.app (that now refuses to open)? Is there a file "error.log" in your yEd.app installation folder? And if so, what's in it?
If not, how did you install the yEd.app from the yEd.dmg? What does it say about ownership and permissions, when you "Get Info" about the yEd.app in the Finder?
Can you open the "yed.jar" by double-clicking it (it's in the yEd.app installation folder, too)?
Can you open the yEd Web Start version from the yEd home page: <http://www.yworks.com/yed>
(the orange "Launch" button).