Your RPM needle resting a little below 1 (1000 rpm) is perfectly normal at a complete stop.
Your engine is actually running on idle around 450 and 700 rpm. Your civic is being provided with just enough gas to keep your engine running before shutting off completely. Otherwise, you would have to restart your car ignition after every complete stop.
Sometimes, you'll notice it above 1 or 2 (1000 or 2000rpm) while at a complete stop. This usually occurs when your engine is cold and your car attempts to try to heat itself up until it reaches normal operating engine temperature.
Hope this helps!