The two countries were united for a time during British colonial rule, but after the Second World War when the UK started granting independence on a wide scale, British India was split up to reflect the religious diversity that existed and still exists.

Religious Map of British India - 1909

Other factors played into the split, such as slightly different cultural and ethnic backgrounds. The reason such animosity exists today was largely because of the violent partition and also the border disputes that followed shortly after, notably in the Kashmir region which is claimed by both countries but in reality China, India, and Pakistan all administrate their own bit.

In conclusion, it's a whole lot of reasons. Before the British came to colonise India, the whole region was even less united than it is now and was host to a large variety of countries.