In case of murder of a PM, the government will quickly select a new one in the matter of weeks. It is a silly political move to kill a PM.
In case of a President, there is a mandate from the population, because he/she was elected directly. And replacing the President is a matter of several months at least, or, in the case of the USA, not at all. And that sends a bigger message to kill a President.
I personally see both system (Prime Minister and President) have pros & cons that doesn't make one better than the other.