The short answer would be - "The Muslim League wanted to create a nation for the Muslims and sikhs did not figure in that"

The real reasons are surely more complicated. I will try to expand on what I mentioned

The Muslim League was formed as a party to further the interests of the muslims. It however did not have much support for a very long time. Even as late as 1939, they did not have much of an electoral impact. The congress on the other hand was more inclusive. It not only had members from various parts of the country, but also various religions. They had enjoyed popular support in Punjab for a long time before the rise of the Muslim League. They were also widely seen as the primary political unit fighting the british colonialism. They wanted to create a secular country with no discrimination against any community.

Muslim League was afraid that in a hindu dominated India the muslims would be discriminated against and a separate country/state was required to safeguard their interests. It gained its power/popularity very quickly on the plank of "Islam in danger". (It is also been argued that they had british support because unless the Congress they supported the British during the World War2). With this plank, everyone who was not muslim became an enemy and the rifts that had existed in India for some time now, were deepened. The Muslim League went on to demand a separate state for muslims while the sikhs did not float a parallel political unit of their own and stuck more or less with the Congress.

It is with this background that the sikh representatives chose to join India instead of joining Pakistan.

Okay, I'm late here, but I'll comment anyway.

Obviously, a separate, sovereign Sikh state would be ideal.

No, it wouldn't. The province of Punjab in undivided India was a Muslim majority. Of the vast state that Punjab was, only the Ludhiana district of Punjab was a Sikh majority. After partition, the Indian Punjab became a Hindu majority. Subsequent Sikh movements led to the division of the state, and Hindu majority areas of Haryana and Himachal Pradesh were separated, and Punjab now was a Sikh majority.

Even so, Sikhs make about 60% of the population of that state, while Hindus, Muslims, and Christians make the remaining 40%. We could go further and end up with a country that would be expressly dependent on India or Pakistan for its existence. Or be placed in the limbo that Kashmir faced.

To put it simply, a Sikh country was simply not viable, and not even seriously demanded during the partition.

Putting things in perspective, Christians make a greater percentage of population in India as compared to Sikhs. And yes, India does have Christian majority states as well, even though they weren't given separate countries in the partition.

Kind of late, but Punjab (the Sikh homeland) as a whole was supposed to go to Pakistan. Promises were made that the Sikhs would have equal rights, but after witnessing some government discrimination (e.g. Favoring the muslim side in land disputes on Gurdwara vs Mosque, only allowing Islamically-slaughtered halal meat [which Sikhs abstain from] in government positions), the Sikhs grew distrustful and clamored for the partition of Punjab with a portion in India. Some wanted a separate country but the British denied the request as it was somewhat ludicrous given their small numbers (even if they had political clout because of being wealthy and well-armed). However, the Nehrus made many promises to ensure the Sikhs would join the secular India, mainly state and religious autonomy.

When Sikhs in the 80s felt as if they were not being given the autonomy they were promised, the Sikh militancy and later Khalistan arose.