I'm not sure how long ago you finished your antibiotics, but they do continue working for some time after you stop. So, if it's only been a day or so, I'd wait and see what happens.
A pilonidal cyst can be painful even if it's not infected. Usually, doctors do not prescribe antibiotics for these cysts. Instead, they need to be drained in order to heal.
The best advice is this: If you're concerned about the cyst, you should go back and see your doctor again. Only he or she can examine the area to determine if the cyst has healed or if it needs further treatment.
Important: The opinions expressed in WebMD User-generated content areas like communities, reviews, ratings, blogs, or WebMD Answers are solely those of the User, who may or may not have medical or scientific training. These opinions do not represent the opinions of WebMD. User-generated content areas are not reviewed by a WebMD physician or any member of the WebMD editorial staff for accuracy, balance, objectivity, or any other reason except for compliance with our Terms and Conditions. Some of these opinions may contain information about treatments or uses of drug products that have not been approved by the U.S. Food and Drug Administration. WebMD does not endorse any specific product, service, or treatment. Do not consider WebMD User-generated content as medical advice. Never delay or disregard seeking professional medical advice from your doctor or other qualified healthcare provider because of something you have read on WebMD. You should always speak with your doctor before you start, stop, or change any prescribed part of your care plan or treatment. WebMD understands that reading individual, real-life experiences can be a helpful resource, but it is never a substitute for professional medical advice, diagnosis, or treatment from a qualified health care provider. If you think you may have a medical emergency, call your doctor or dial 911 immediately.