I think you mean "East Pakistan," but nevertheless the reasons for the war were numerous. Bengalis actually comprised the majority of the Pakistani population at that time, but they were being treated more or less like a colony by West Pakistan which controlled the organs of the state. By this I mean they extracted resources and tax revenue from East Pakistan to develop industry and militarily defend West Pakistan. In the 1970 election Sheikh Mujibur Rahman and the Awami League won over Zulfikar Ali Bhutto and the Pakistan People's Party, but the state refused to acknowledge the election outcomes. At the same time, Mujibur and the AL were demanding a new constitution which would grant more power to the various regions of Pakistan, which was unacceptable to the West Pakistanis. Then there is the language issue as well. From the very start Jinnah had been trying to introduce Urdu into East Pakistan as the language of teaching and administration, which was seen as an attack on the Bengali language, which the Bengali people are extremely proud and defensive of especially after the Bengali Language Movement of the 1950s, which West Pakistan also used coercive police power to suppress.

So the background of the war was very heated in a purely political and ideological sense. On top of this, East and West Pakistani cultures were very different. East Pakistani Islam was heavily intermingled with what we might call "Hindu" cultural forms. They were seen by the West Pakistanis as generally bad muslims, or even closeted Hindus and secret allies of the Indians. West Pakistani leaders made such public accusations of Mujibur. At the time there were also a lot more Hindus in East Pakistan than currently exist. In the 1950s they were a little over 20% of the population, and were generally a wealthier and more educated class. The Pakistanis considered these people to be a 5th column within their ranks who were manipulating local politics to their advantage. The genocide which they launched in Bangladesh did kill plenty of Muslims, but it was also disproportionately targeted at Bengali Hindus, and those thought to be under the influence of Bengali Hindus. Also, once the war started and it became obvious that the emergent Bangladeshi state would be a secular one, it became obvious that Bangladesh was directly contradicting the core foundational principle of Pakistan. The idea of a secular socialist republic breaking away from an Islamic nation was also threatening to Islamic regimes generally, so almost all of the Muslim world sided with Pakistan during the conflict.

Beyond these factors, I cannot account for the extreme level of brutality of the Pakistani military towards the Bengali population. The causes for the war are clear, and one can see why the Pakistanis would have animosity towards the Bengalis but the sheer magnitude of the violence seems to defy explanation.