"Seems to be the problem area, doesn't it? We keep hearing about it. Why bother with more civilized parts of Afghanistan, send the military to where Al-Quaida and the Taliban lives. To borrow a quote "We can do more damage that way"."

If you wanted to know, I would suggest you read "In the Line of Fire" by Pervez Musharraf. I don't recommend the book because the author is a good writer. But it does offer his view and it's probably [almost certainly] is colored by an attempt to sell his "cause" to an American/European audience. Musharraf is apparently a well trained military officer. One thing he claims is that he has an aversion to the act of declaring martial law [and apparently didn't do this]. Why he claims this could be because of Pakistan's past experience with martial laws, and/or because of his reading of Pakistan's constitution, and/or because he thinks other nations [US or world opinion] frowns on this.
Now he was the top military commander of Pakistan who basically claims he [and more importantly the Pakistan military] resisted a coup against him, by the elected civilian leader

A couple things to understand is the Pakistan is a "relatively" new country [as are many countries in the world]. And Pakistan separated from India and then after this Pakistan divided into Pakistan and Bangladesh:

"resulted in the independence of Bangladesh under the leadership of Sheikh Mujibur Rahman in 1971 after the bloody Bangladesh Liberation War, in which it was supported by India. The years following independence have been marked by political turmoil, with thirteen different heads of government, and at least four military coups."
http://en.wikipedia.org/wiki/Bangladesh
Hmm, I wonder what Wiki says about Pakistan. Selected quotes:

"The name "Pakistan" means "Land of the Pure" "
...
"Pakistan is the sixth most populous country in the world and is the second most populous country with a Muslim majority."
...
"Economic and political dissent in East Pakistan led to violent political repression and tensions escalating into civil war[15] (Bangladesh Liberation War) and the Indo-Pakistani War of 1971 and ultimately the secession of East Pakistan as the independent state of Bangladesh.[16]

Civilian rule resumed from 1972 to 1977 under Zulfikar Ali Bhutto, until he was deposed and later sentenced to death in what amounted to a judicial murder in 1979 by General Zia-ul-Haq, who became the third military president. Pakistan's secular policies were replaced by Zia's introduction of the Islamic Shariah legal code, which increased religious influences on the civil service and the military. With the death of General Zia in a plane crash in 1988, Benazir Bhutto, daughter of Zulfikar Ali Bhutto, was elected as the first female Prime Minister of Pakistan. Over the next decade, she alternated power with Nawaz Sharif, as the country's political and economic situation worsened. Pakistan sent 5,000 troops to the 1991 Gulf War as part of a US led coalition and specifically for the defence of Saudi Arabia.[17] Military tensions in the Kargil conflict[18] with India were followed by a Pakistani military coup d'état in 1999 [19] in which General Pervez Musharraf assumed executive powers. In 2001, Musharraf named himself President after the forced resignation of Rafiq Tarar. After the 2002 parliamentary elections, Musharraf transferred executive powers to newly elected Prime Minister Zafarullah Khan Jamali, who was succeeded in the 2004 Prime-Ministerial election by a professional banker Shaukat Aziz, followed by a brief (temporary) stint in the seat by Chaudhy Shuja'at Hussain."
http://en.wikipedia.org/wiki/Pakistan