Not sure if this holds true for everyone, but each time I have done this quest or "Pluck Them All" I have never gotten more than one Rune.
From the Runic Pouch description:
for your current class specialization."
"Runes"; as in plural... meaning more than one. Might as well not even be a bag if all it contains is one Rune. :-P
Eight hours to complete, rewards one Rune. IMO, you're better off doing LFR if you're after Runes.
Garrison Timer Mobile App
[Upon completion your 随从 will gain: ]
Missions and Followers math for maximising success chance
Patch 6.1 Garrison Changes
Warlords of Draenor Garrison Missions Guide