In my opinion it was because of the vulnerability of the City. It was on the coast line and India too. It could have been easily attacked and since we were and are in a state of war with India almost every time so it would be a bad idea to put the Capital on risk. As they say, if the Capital falls, the entire country falls.

1 main reason is that Ayub wanted to live near GHQ which is located in Rawalpindi. So, He decided to make capital in near to GHQ. In other side, Karachi is a commercial hub of Pakistan and Ayub was wanted to build a capital where a peaceful place and also low population.

"This move by Ayub, as most moves and actions of Pakistan’s successive leaders, was more in his own interest than in the nation or the country’s interest. A prime reason for shift was that being near the army headquarters would allow the dictator to keep an eye for any adventurous moves within the army against him. Also, Ayub visualized a long term role in governance for army and moved the capital to be near the GHQ and not the GHQ, for ‘strategic’ reasons, to be near Karachi.
The shifting was opposed by East Pakistan, also by the smaller provinces and territories in the west, who viewed the new capital, at its assigned location, as reinforcement of their frustrations at the domination of the country by the largest province in West Pakistan, and by the army.
The inborn fissures Pakistan was born with required delicate handling. The foremost pickle was two Pakistans, East and West, a thousand miles apart with majority of Pakistanis living in the territorially smaller part, or East Pakistan. There was also the sticky situation of smaller provinces gripe, not entirely unfounded, of being shortchanged by the largest province in West Pakistan. These issues called for political handling, which got precluded by Ayub’s 1958 takeover.
The country as a whole had settled down with Karachi as its capital. The city came to belong to all, and the large hearted people of Sind accepted it too. A clumsy attempt to declare Karachi a separate province was made immediately after independence, which the people of Sind rightly resisted, and the political government of the time wisely discarded the move.
Karachi had become a ‘melting pot’ for the country, it belonged to all and it helped bond the people as a nation. For the smaller provinces and territories Islamabad is a distant vision belonging to the ‘privileged’, or to the ‘more equals’. Far from creating a feeling of belonging as did Karachi, Islamabad’s instatement as capital drove wedges between people, at least one of which sundered the country.
Islamabad’s nearness to army headquarters, and with air force and naval headquarters also moved there, may have been source of comfort to military rulers, but it never acquired the status of Karachi, as a national ‘melting pot’, a city belonging to all. East Pakistan is no more, which it may still be had Karachi remained the ‘melting pot’.
Islamabad, almost as an ‘exclusive’ city, has cut off the rulers and the bureaucracy from the people, whose problems they are supposed to help resolve. Unlike Karachi, where the wretchedness of life in the country was not hidden, living and working in Islamabad is like being cocooned from it. Over the years this has changed the psyche of the rulers, and the bureaucracy. Their ‘living in Islamabad’ experience has made them impervious to the hardships of people, caused by living in a corrupt, shoddily governed country.
Islamabad also cocoons the rulers and the bureaucracy from accountability. What the rulers and the bureaucracy get away with in Islamabad, it would have been hard for them to do in the glare, and stare, of Karachi
Try as one would, it is hard to find any benefit to the country of erecting Islamabad as the new national capital. The divisions and mess it helped create are something the country could have well done without. But the deed is done, and it is irreversible.
For probably the first time, however, there is honor in the air in Islamabad. It has come through the Judiciary. if the Election Commission of Pakistan, and the National Accountability Board, the so called NAB, also join in creating honor for Islamabad through fair elections in full compliance of constitutional stipulations for these, through just and fearless accountability of past scams, that would help freshen the air in Islamabad even more. Unfortunately, its capital, Islamabad, has so far remained the prime source of ignominy for Islamic Republic of Pakistan.
Islamabad could do with cleansing actions with a hard brush by as many institutions as have the courage to do their duty. So far only the judiciary has shown courage."
SKH

Weather and climatic conditions also played part.

Due to least population but know people move and live there.so i things strategy of Ayoub is done well know according to current situation of pakistan

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