What were Aurangzeb Alamgir's motives for reversing much of the religious tolerance in the Mughal Empire?

Political expediency.

A common, populist explanation is that Aurangzeb Alamgir was religiously conservative, as taninamdar has noted. However, this is certainly not the whole picture. Though his personal religious outlook may well have been an underlying bias, political considerations were at least equally important reasons for Aurangzeb's policies - if not the driving motivation.

His intolerant religious outlook has been attributed not merely to his own personal inclinations, but to compulsions of state, primarily the need to get the support of the ulama and nobles.

_{- Dalal, Roshen. The Religions of India: A Concise Guide to Nine Major Faiths. New Delhi: Penguin, 2010.}

Note that he did not actually restore the jizya tax until 1679, and this was suspended after 1704. When the jizya tax was being collected, it was also earmarked for charity. It was apparently an unemployment relief project designed to bribe the clergy for political reasons.

Jizyah was not only meant to be a concession to the clerical opinion, but implied a huge bribe to them whereby Aurangzeb hoped to use them as a means of rallying Muslim opinion behind him for any projected action against the Muslim Deccan states.

_{- Chandra, Satish. Essays on Medieval Indian History. Delhi: Oxford University Press, 2003.}

In fact, throughout his reign, Aurangzeb readily disregarded religious demands in favour of the needs of the state.

Even though he was well versed in the religious sciences and led an austere life, he did not allow religion to encroach on the interests of the empire, and even went against the letter of the [religious] law when the reasons of the state demanded it.

_{- Markovits, Claude, ed. A History of Modern India, 1480-1950. Anthem Press, 2004.}

An illuminating case is his response when a group of Muslims and Hindus were found guilty of sedition.

The qazi decreed that the Muslims should receive light punishments and the Hindus be released on condition that they converted. Aurangzeb's response was brusque: 'This decision is according to the Hanafi school; decide the case in some other way, [in order] that control over the kingdom might not be lost.' In putting the safety of the realm first, he mirrored the priorities of his supposed opposite, Akbar.

_{- Copland, Ian, et al. A History of State and Religion in India. Routledge, 2013.}

He didn't really reverse that much.

Despite the reputation, Aurangzeb's supposedly hardline religious policy was but a phase in his long reign. There was no major discrimination against non-Muslims in the first years of his reign, and after an interruption and he returned to this conciliatory stance later. In his last will and testatment, Aurangzeb called on his successors to continue the pluralistic policies started by Akbar.

His testament does not give religion a predominant place. It contains many references to Shah Jahan and even to Akbar, and advises to follow their conciliatory policy. Aurangzeb thus emphasizes continuise with his predecessors and not the rupture that had marked the middle of his reign.

_{- Markovits, Claude, ed. A History of Modern India, 1480-1950. Anthem Press, 2004.}

To a large extent his image as a bigot has been the result of exaggerated accounts, not historical facts. Even the popular impression of Aurangzeb as a tyrant destroyer of temples is only supported by scant contemporary evidence. Instead, Aurangzeb made donations to and issued edicts protecting temples, even building some himself.

Even Aurangzeb, infamous in the old historiography as a destroyer of temples, actually built many more than he destroyed.

_{- Copland, Ian, et al. A History of State and Religion in India. Routledge, 2013.}