The gemara on the bottom of Bava Kama 38b - top of 39a says that although R. Meir should penalize one who rapes a kutit and not obligate the raper to pay a penalty of 50 shkalim to her father, so that the kutim will not be "hidden" within Israel, he does not apply the penalty here in order "shelo yihe choteh niskar" (that the sinner shall not benefit from his sin). If that is true, then why on 38b does R. Meir put a penalty in the case where the Jew's animal gores the kuti's animal (that he is exempt from paying), isn't this also a case where the sinner is benefiting? In other words isn't the Jew a sinner for letting his animal gore a kuti's animal and yet R. Meir does not obligate the Jew to pay (hence giving him a benefit) in order that the Kuti does not become "hidden" within Israel?
Negligence, although one is liable for it, does not constitute sin. Your term "letting him gore" is slightly misleading, for it was his negligence which allowed the animal to gore. One is responsible to watch his animal, and is liable if it damages; however, we need not penalize him if it does not cause damage for which he is liable.
In addition, although one is required to watch his animal, its damages are not a premeditated act such as the Ones of a Kusis, and therefore there is less need to penalize him.
D. Zupnik