Then why is it that Jotun militia, especially, is widely reputed for its cowardice?
I'm sure Arryn has run into this at some point before: Jotun militia, I've found, is notorious for its tendency to break and run from battles that it could have otherwise won. Jotuns generally are more susceptible to morale failure, despite their individually higher morale, for several reasons:
#1: Their high hitpoints mean that they frequently survive hits, which force a morale check for being injured.
#2: Their higher cost means you'll have less of them in the squad, so they don't have the same level of large-squad buffering.
#3: Their large size means that relatively few Jotuns will form a line compared to the masses of smaller units that swarm you. A single Jotun will end up fighting at least 3 humans.
#4: Last but not least, large units running in terror are more noticeable.
It's easier to gain a reputation for cowardice when all eyes are on you as you bravely run away. And when they run, they take a larger amount of fighting power with them.
So, as a general rule, given units of equal morale, say, a Jotun with morale 11, and humans with morale 11, the Jotuns are more likely to cut and run.