90% of ammonia tests test for total ammonia-nitrogen. Total ammonia-nitrogen is comprised of ammonia (NH3) and ammonium (NH4+). NH3 is "free-ammonia" and is highly toxic to fish and other animals. NH4+ is "bound-ammonia" and is totally harmless. Both kinds exist in the aquarium simultaneously. Depending on the pH and temerature of your water, You can safely have a specific amount of ammonia on your test kit without it being toxic.
The chart below shows you the maximum amount of ammonia that is, or can be in the ionized form NH4+ (ammonium), according to pH and temp. In short, you are "allowed" to have this much ammonia without it being harmful to your fish:
If you regularly test and find ammonia on the test results, something is amiss and investigating is in order.
I hope this helps!