Urine tests are extremely accurate but sometimes if you are very early in your pregnancy you don't have enough of the hormone in your system for it to register, but I am sure the nurse would have told you all this and if she is confident you are not pregnant I would be apt to believing her. Chances are by the sounds of things your naturally irregular periods, new exercise regime and stress about the mishap (unprotected sex). Have lead to the perfect storm of causing a disruption to your cycle. Honestly the more you worry, the less likely your period is to return, my advice: relax, slack off the workout for a week or two and your monthly visitor will be returning in no time (and you'll be wondering why you wished for it, lol).
Try some deep breathing exercises or some escapism with a favorite book or movie and take a relaxing bath or something, remember you can't change the past so there is no sense losing sleep over it.
On another note, please, please, please get some kind of reliable birth control method, if there is even the slightest chance you may have unprotected sex again it is much better to be safe than sorry. Although the barrier method is always best (condoms) since there are worse things that can happen than an unwanted pregnancy but it doesn't hurt to take a birth control pill once a day just in case.
Thank you so much for your response it makes a lot of sense to me more now . I will try to relax more, and yeah i know i have to use some type of birth control, i'm not even a sexually active person its been about 10 months since i haven't had sex and BAM i have sex just 2 or 3 weeks ago and this happened . And i was worrying a lot but soon after i received that "Negative" result from the nurse it calmed my nerves a little i just hope to get it soon, and i'm trying my best not to over think or stress any more then i already have :)