Well when I have had upper respiratory infections, I was told by my doctor not to exercise so that it would not spread to the lower respiratory organs.
Same for ear, nose, eye and some skin infections the advice and signs at the public swimming baths say not to go swimming.
I am not a doctor, but am only quoting what a professional doctor's advice given to me.
But to me it does make sense not to exert the body and to rest it to allow for the body to recover quicker. Of course it depends on the site of the infection and how ill the person feels.
If you have information to back up your comments of "No So!" perhaps you could explain it to us.
Best wishes
"by exercising you may have been further spreading the bacteria around your system" Not So!
In your case because you had not been to the gym for a long time, your sore shoulder muscles may have nothing to do with the cipro and it may just be coincidental.
When you have not exercised for a long time and then start to exercise again, everything feels sore and tender.
Had you been exercising at the gym non stop and got the muscle soreness when taking the cipro, then yes, I would have suspected that may have been a side effect from the cipro.
Whilst you are ill with an infection and on an antibiotic, you should not be doing strenuous exercises anyway. You should give your body time to heal and take things easy. Also by exercising you may have been further spreading the bacteria around your system.
Wait until you have finished the course of antibiotics and when you are well before going back to the gym. You will, I hope, be familiar to do warm up exercises before doing any gym work.
Best wishes.
Cipro can cause tendon problems - some have torn or broken the achilles tendon by stepping down too hard while taking Cipro. You will usually feel that the tendon is hard as a rock - if you feel that, wait to exercise, until you have stopped taking the antibiotic.
You may have to switch to a different antibiotic - see your doctor.
I suggest asking your doctor when can you return to the gym.