Because if you have and addiction to something, and you stop, you can have body achs. For example, if you drink coffee and forget to drink it one morning, you have body achs because you are so used to what you were doing.
Just like a drug addict, someone who quits taking nicotine goes through withdrawal. As you know, this is very unpleasant. The good news is that it will fade away over time. Also, your body has not yet begun to heal the damage done by smoking, which will also make you feel better.
Speaking as a former smoker, your body is trying to adjust to your new, nicotine-and-tar free lifestyle. It will take time (especially if you were a long term smoker), but you can take comfort in knowing that you won't feel "worse" forever.