I'm not sure that's particularly personal on the army's part though, I get the impression they're happy to stand behind pretty much any government for a while, and then once that party start getting ideas they turn on them and get rid.
Looking at the opinion polls listed on Wikipedia, the...
At the last election his party only won about 32% of the vote.
A quick skim of the Wikipedia page seems to suggest that every party involved claimed there was some bias against them.
I think he's always been more controversial in Pakistan than might be imagined.