So, a Knight, Noble or Priest with Fame is simple enough - but Senior clergy start with a reputation of 4 by default. Is fame additive, or a second reputation?
What is the effect of Temporal influence? It seems by default a Landed Noble, Priest, or Senior Clergy would already have some temporal influence already, so would taking the virtue make for a very influential character?
Now, Protection in the case of a Knight or Landed Noble implies a feudal lord looking after them. Similarly with Priest, implies they have the favor of a Bishop - but what of a senior clergy, the pope?
The Church book (p28, box text at top of page) states if you wish to play an archbishop or cardinal, you must take Senior Clergy social status and Temporal Influence as required Virtues. (I looked into this while trying to create a priest with as much magic resistance as possible. While theoretically our covenant controls a cathedral school, our SG felt having an Archbishop as a companion might be stretching things).
Fame - if you already have a reputation of 4 from other things, presumably fame adds another one - so your priest can be famous as a theological scholar or as someone whose intervention stopped a war.
Protection - for senior clergy this would indicate maybe the pope or a cardinal is looking out for you, or maybe you have a mundane king or Holy Roman Emperor who wants to look after you. (Perhaps you're a junior member of a powerful noble family who was sent to join the church?) For landed nobility, protection would be either someone at the highest levels of nobility protecting you, or having a friendly bishop/archbishop pleading your case in ecclesiastical matters.
I would probably rule that if multiple Virtues or Flaws give Reputations, then they are separate. So a Bishop Max with Fame could have both Reputation (Bishop of Norwich) 4 and Reputation (miracle worker) 4.
Temporal Influence includes the personal ear of other influential people. So while a Baron is influential in his own right as a noble, a Baron with Temporal Influence (who is the godfather of the King's Chancellor) has much more sway. A bishop who avoids politics at the King's court will have less pull than a "mere" priest who's been appointed as the King's personal confessor, for instance.
The Protection Virtue I'd say goes beyond the traditional feudal relationship. The feudal relationship is the default, so in theory a knight could count on protection by his Baron. That's going to be folded into the Landed Knight Virtue. However, if Thomas de Alvi, Crusader, Baron of Blackhill, and famed swordsman is your liege and personal drinking buddy... then that counts for more than a pro forma relationship with your liege (and thus worth a Virtue). Protection means you have a powerful person looking out for you and it's somewhat understood that you fall under his umbrella. This is not always someone who is a social superior, just someone with power.
On checking Lords of Men, it suggests on page 7 what virtues you should have - and it specifically lists Temporal Influence for officers, and again in the Officers section, so if your noble wants to be King's marshal or an admiral as well, Temporal influence is the virtue to take.
Not all Senior Clergy have much temporal influence. For example, an abbot might not have much impact outside his abbey, even a bishop might not have much influence outside his court. It all depends on the local context.
Of course, many senior clergymen do have temporal influence, which is why The Church recommends it as a Virtue for senior clergymen, but some don't, so don't take the Virtue for those ones.
The source of Protection doesn't need to match the "job" of the character; as Renimar says it more represents Protection in addition to the normal feudal relationships (or at least much more enthusiastic protection than would be expected under normal feudal relationships). The Protector of a priest could be a baron. The Protector of a baron could be a bishop. The Protector of a bishop could be a duke. Equally, the Protector of a bishop could be another senior clergyman (the grandmaster of a military order or an archbishop, for example). Or a bishop's Protector could be a magus. Or a bishop's Protector could be an important guildmaster in the city. Or whatever...
I would say, it depends on what he is specifically famous for and as.
For a famous bishop (great theologian, excommunicated the king, saved Jews from pogrom, etc) the Fame reputation might be additive. For a famous person (led an army, slew a dragon, married a witch, etc) who later became a bishop, then the reputations might be separate.