Since there is no official explanation available from the US side, the only explanation I can guess is that the USA saw Pakistan's attack on India in 1965 as a possible shift of balance of power in favor of communist China.
Until 1969, the USA was adopting a policy of the containment of China:
Washington encouraged its allies to refrain from entering into diplomatic relations with Beijing. The United States prohibited Americans from visiting China. The United States cut off trade and orchestrated an international embargo of China.
By being even tougher on China than on its main communist rival, the Soviet Union, the United States pursued a so-called "wedge strategy." This strategy aimed to encourage a split between the two communist allies. It was successful because such a split did occur, becoming evident in around 1960 and worsening thereafter.
Pakistan was a member of US-led anti-communist pole (SEATO, CENTO, etc) from its inception.
Due to the common hostility with India, Pakistan started to warm relations with China ("An enemy of my enemy is my friend"). The progress was steady and significant:
- 1950 - Establishment of diplomatic relations with China.
- 1962 - Sino-Indian war where India lost miserably.
- 1963 - Resolution of land disputes with China by ceding disputed lands.
When the 1965's Indo-Pakistan War broke out, Pakistan didn't receive any direct help from the USA. This put the US-Pakistan alliance in question. So, Pakistan decided to leave SEATO/CENTO pact.
The USA saw the leaving of the pacts and the warming up of the relationship with China as duplicity from the Pakistani side for two reasons:
- Pakistan's act was against the China-containment policy of the USA
- Pakistan-China alliance was seen as the shift the balance of power
#2 begs an explanation.
India was a nonaligned country, so it posed no threat to the USA. India was a democracy and had an enormous population, but India also had close ties with the USSR. So, any imbalance of power in the region had the possibility to either push India more to the USSR's sphere or making China stronger. That was a big risk factor for the USA. So, given its democracy and stable domestic political environment, strategically, India was considered by the USA to be the leader of South Asia. As a result, the Indian occupation of Hyderabad, Junagarh, and Goa, and` blatant intervention in Sri Lanka's civil war and in Maldives' coup de tat never raised any eye braw from the West.
Initially, the USA sought a close relationship with India but India refused.:
Nehru and his top aide V. K. Krishna Menon discussed whether India should "align with the United States 'somewhat' and build up our economic and military strength." The Truman administration was quite favorable and indicated it would give Nehru anything he asked for. He proudly refused and thereby forfeited the chance for a gift of one million tons of wheat. The American Secretary of State Dean Acheson recognized Nehru's potential world role but added that he was "one of the most difficult men with whom I have ever had to deal." The American visit had some benefits in that Nehru gained widespread understanding and support for his nation, and he himself gained a much deeper understanding of the American outlook.
India rejected the American advice that it should not recognize the Communist conquest of China, but it did back the US when it supported the 1950 United States.
On the other hand, Pakistan's alliance with the USA was a superficial one just like the Gulf states, where there are no shared values including the religion. So, when Pakistan attacked India in 1965, the USA considered this as a trigger for the rise of a second communist power which was China.
This argument hasn't lost its relevance even today. The current US policy seems to contain China while Pakistan and India are sitting at the opposite camps when it comes to the USA's China-containment policy.
After 1969, the USA changed its policy toward China and decided to help china to pit it against the USSR by supplying arms, technology, and investment.