By default, OneNote 2010 starts with Windows logon, however, if you don’t want to let it run each time you log into Windows, you can easily disable it to remove its icon from taskbar. OneNote 2010 offers a simple way to remove only the taskbar icon instead.
To remove OneNote icon from system tray, on File menu, click Options.
It will bring up OneNote Options dialog. From left sidebar, select Display and from main window disable Place OneNote icon in the notification area of the taskbar option. Click OK to remove icon from system tray.