Pillarisation has its roots in the 17th century, but it did not come into existence until the late 19th century, and lasted until the late 1960s. Coincidentally, it was started by the first national political party that the Netherlands had. Before the 1870s, the Dutch parliament only consisted of individual members, even though all political power had effectively been switched from the king to the parliament in the 1848 revolution, and Thorbecke's Constitution. The majority of the parliament was (classical) liberal, due to the franchise being restricted, and the liberals held on to the principle that each parliamentarian should be independent (this is in fact enshrined in the Constitution).

The struggle between the royalists and the liberals that ended in 1848 took on a somewhat different form after the decisive liberal victory, transforming into a struggle between the protestant politicians who wanted a theocracy and liberals. A key demand of the protestants was equal funding for religious schools, around which the first political party was organised. This was the Anti-Revolutionary Party, which was formed in 1879. Incidentally, its name is intended as a rejection of the values of the French revolution.

The idea of the ARP, as the wikipedia article suggests, changed from establishing a theocracy to ensuring 'sovereignty in [its] own sphere'. This was gradually adopted by the other groups, Catholics and Socialists, although the liberals were never too happy with it.

This is the political part. Another part is social/economic. Pillarisation would have been more difficult to establish in a pre-industrial, rural society, and the industrialisation, and mass move of people from the countryside only really took off in the 1880s (in The Netherlands). Most of the aspects of pillarisation require a modern, somewhat literate society.

Did this lead to our fragmented political landscape? I don't know. In part, maybe, but there were only three real pillars plus the liberals. I think that the fragmentation is more due to the splintering of the protestant churches. Each church sort of got its own party. Another part is due to the fact that we have a proportional representation system (for the main chamber of parliament) without an election threshold beyond the requirement of getting 1 out of 150 seats, which will naturally lead to some degree of fragmentation.

It's an interesting question how this institutional setting interacts with the social reality. In a district-based first past the post system, there would probably have been less splits between the protestants (also on the church level), and they would probably have merged with the catholics a lot earlier.