Remove shrubs and plants from around basement windows to make them more visible, or install thorny bushes around the windows to deter burglars.
Place window-well covers over the wells of basement windows and install a locking system inside the well. This locks the window well, but since you can unlock it from the inside it doesn't prevent you from using it as a fire escape.
Install keyless locks or security bars on the windows to prevent entry, but keep them easy to open in case you need to escape.
Replace the basement windows with shatterproof glass or apply a security film to the windows. Both prevent the windows from shattering when struck by a hard object.