Do you have any specific examples of underrated Emperors? Most of the rulers of the Byzantine Empire were not fit for the job (the Angelos, for one), and only a few emerged with any kind of ability (the Macedonian Dynasty, for example). Even famous rulers like Justinian I had many, many flaws in their leadership abilities. Instead of saving his gold for an army to defeat the Persians and acquire valuable cities and unchallenged population centers, he paid the Persians off and then focused on the perilous areas in the west - thus wasting massive amounts of money and manpower.
This is just one example, and I'm not saying that perhaps they should have slightly better ratings in some cases, it's just that Byzantium lacked strong leadership through most of its history.
