First of all, Borneo is currently divided between three nations, Brunei (which is located entirely on the island) Malaysia and Indonesia.

The way the island was divided was based on the previous colonial governments. Indonesia became independent from the Netherlands in the 1940's, and the new government claimed all of the former Dutch East Indies, including Kalimantan.

The Northern part of the island was divided up between British colony North Borneo (now Sabah), and the British protectorates of Sarawak (ruled by a royal family of British descent) and Brunei (a native state that had existed on the island for centuries).

All these areas remained British until the 1960's and there were efforts to unite the former British territories in the region into a united nation for Malays, that became Malaysia. Sarawak and North Borneo went with Malaysia, Brunei backed out, as did Singapore.

However, Indonesia wanted to rule the whole island, and there was a period of low-level warfare called the Confrontation, between Malaysia and Brunei (backed by Britain and other Commonwealth countries) and Indonesia during the 1960's.

Overall the reason there is not Bornean state is because

1. Indonesia and Malaysia don't particularly want to give up their land, especially considering how rich in oil Borneo is.
2. There is no real "Bornean" identity. The island is home to Dayaks, who are subdivided into many different groups, Malays, Chinese, Banjar and others.

They have no more reason to want a Bornean state than Europeans to want a European state, or South Americans to want a single nation.

There is nothing pushing them together, and three nations pulling them apart. Four, if you count the Philippines who claim they have a right to Sabah.