The punitive system of the Torah was arranged in such a manner, that only a violation of negative commandments, carried with it a punishment. The only exceptions were the non-fulfillment of circumcision as well as not offering the Pesach sacrifice. These two instances were dealt with in the Heavenly court where כרת, or being cut off from the Jewish people, was administered.
Of the 365 negative commandments, 207 are punishable with lashes. The remaining violations are either so severe that capital punishment is administered, or lesser violations that require the payment of a penalty. For example, the thief will pay double what he stole.
There is also a concept called, קים ליה בדרבה מימיה. This means that if one does two infractions at the same time, he is punished for the more severe infraction.
The classic example would be one who stole on Shabbat, and carried the stolen object from a private to a public domain. Shabbat violation is more strict, as the Torah punishes with death by stoning for Shabbat desecration. Therefore, our principle exempts the thief from paying for his theft, since he must deal with the more severe violation.
Principles such as these must be studied thoroughly in the Talmud, to fully appreciate the wisdom behind it.