Yes. You can run NetBeans with the --fontsize <size> option. The default <size> value is 11. You can set it to 12 or even a higher value and see if it works better for you. The --fontsize argument applies to fonts used in menus, dialogs and most components in the IDE.
The size of fonts used in editors is also based on the --fontsize parameter as long as has not been customized by the user in Tools | Options | Editing | Editor Settings.
To set this option permanently, edit netbeans.conf file.
Note that NetBeans 6.1 running under Gnome with the GTK L&F uses the default Gnome settings including font size. If you want to change the font size for NetBeans you must change font size in Gnome Preferences -> Application Font. Alternatively you must use Metal L&F with --fontsize option. Use --laf jvax.swing.plaf.metal.MetalLookAndFeel to run with Metal.
netbeans --fontsize 14
Applies to: NetBeans 3.6, 4.0, 4.1, 5.0, 6.0
Platforms: All
See the entry in the developer FAQ.