I found a workaround for styling the menu when not using the treeview. If you switch to subblue skin, you will see the menu there is styled ok. I think your skin from your screenshot was based on subblue but with a horizontal menu, you would need to set Orientation=Horizontal on the mojoMenu in App_Themes/default/theme.skin
There are actually 2 issues at hand, the first is that ControlAdapters are not working so the menus render as tables. The second is that the VirtualPathProvider is not working on Mono so when you try to style the menu or the treeview with theme.skin file, it does not use the one from your skin folder, instead it uses theme.skin from App_Themes/default/theme.skin so you have to make your customizations there to style the menu. I have updated App_Themes/default/theme.skin to look ok with subblue skin but you could comment out the settings and then modify to suit a different skin. css files still come from the skin folder as no virtual path provider is needed to make that happen.
Another side effect of this VirtualPathProvider not working is if you customize the App_Themes/default/theme.skin file, any child sites will also use this theme so unintended style results may occur in child sites.
These changes should be in svn trunk within the next few hours and should at least provide a little better style.