Muslims had ruled India, or major parts of it, for many centuries before Britain displaced them. Hindus had gained ground during the British occupation, but Muslims still had a large presence in the Army, the civil service, and as land owners. Independence brought the threat, or at least the imagined threat, that they would be a submerged presence in the overwhelmingly Hindu population under democratic rule. Pakistan was created as an answer to this perception.
That one idea, of being Not India, was a very fragile premise on which to build a nation. Pakistan inherited a big expensive chunk of the Indian Army, but not the resources to fund it. Because the army and the civil service were the institutions of the elite who founded Pakistan, ways had to be found to fund them. Pakistan's solution was to tap into the US treasury on the dubious premise of being a bulwark against Communism and keep its people distracted with fulminations against India.
To Eisenhower and his military people, the British educated Pakistani military leaders were more personally compatible than the neutralist and socialist Nehru. Despite well founded doubts about the value of Pakistan as an ally, they mostly kept the gravy train running for the Pakistani military. Meanwhile, these military rulers did essentially nothing to advance Pakistan's economic development, finding it easier to fan religious fanaticism.
Kennedy proved a more resistant President. When India went to war with China, the US rushed military aid to India, outraging Pakistan, which saw the war as a chance to pursue its long time objectives in Kashmir. Pakistan's leaders stirred up public sentiment against the US while protesting to the US that they faced a popular revolt if the US would not be more cooperative. It was a double game which had appeared before and would again.