Pilonidal cysts = incredibly painful! So sorry you're going through that (I had this happen - resolved itself non-surgically, but recurred twice and was some of the worst pain I'd ever experienced).
OK, so you can't do bouncy/high impact exercise or lower body workouts. Can you lift upper body? Can you walk? A lot of doctors will initially say "you need to rest" and not give specifics...I've had a lot of luck saying "Physical activity is very important to me - what options do I have to stay active without delaying healing". Once you say it is important, they'll usually suggest alternatives except in dire situations when ANY movement is bad, so try asking for more specifics.
If they say you really CAN'T move, then sure, it's a setback, but it isn't insurmountable. You definitely won't lose all of your endurance in a few weeks, and even if you did, you built it once, and you can build it back up again. Setbacks happen, but they don't have to derail you. Watch your diet, return to exercise when it is safe to do so, and let your body heal.