You don't have to be friends to be allies. During WWII, we were allied with the Soviets, who were obviously our enemy from the day the Bolsheviks took power. We allied with the Khmer Rouge, another enemy, to get Vietnam to leave Cambodia. We allied with China, yet another enemy, to help supply the Afghan resistance during the Afghan-Soviet War. Foreign policy is no different from the life of any small business owner. There are multiple adversaries popping up all the time, and there is no end to them.
In most wars, past and present, none of the participants were/are people we would consider to be “good guys.” Most would be considered to be bad guys. Right now, ISIS seems to be the worst of the bad guys. Assad has no intentions of conquering the world, but his backers in Iran do. So we would be careful, keep our eyes open, and our powder dry.