The main driver of the Italian unification process was a peculiar union of certain segments of the Italian nobility and the urban bourgeoisie, and both were aggressively secular.

It's important to note that it was the French Emperor Napoleon, through his conquest of the ten 18th century successors of the medieval Italian city-states (including the Papal States) who lay the definitive foundation for what would become modern Italy. In spite of the three-way administrative division, Italy under Napoleon was united for the first time nearly a thousand years, and devoid of economic/customs barriers: After Napoleon’s conquest of the peninsula, Northwestern Italy was integrated with the French Empire, while the northeast was proclaimed "The Kingdom of Italy," with Napoleon crowned king. The south remained the Kingdom of Naples, ruled by Napoleon’s brother-in-law; Joachim Murat. In all three polities, Napoleon abolished old ecclesiastical and aristocratic privileges and imposed uniform legal, administrative, and fiscal laws and institutions. All three polities were administered by a large and meritocratic governmental bureaucracy. What's more, Napoleon was also a very aggressive secularizer: many museums in Italy have their roots in the art and treasure seized from churches and clergymen in the Napoleonic era (not to mention about half the items in the Louvre).

After Napoleon restoration, intellectuals from all over Italy migrated to the Kingdom of Piedmont-Sardinia. Although initially repressive, the government in Turin soon cautiously acknowledged their value. Previously one of the more marginal states in Italian history, the Piedmontese already had a precedent for acknowledging and adopting the practices of their more powerful neighbors; welcoming prominent exiles wasn’t too much of a stretch. These intellectuals would not only supply the Turinese government with a full roster of capable public administrators who fueled its economic and intellectual life, but they also shaped public opinion enticed Piedmont it to take action bringing about the unification of Italy. Many of these intellectuals were middle class and had been rewarded by Napoleon's meritocratic military, education system, and state bureaucracy, which had opened career paths previously only open to upper-class twats. Similarly, many intellectuals had no qualms reducing the role of the clergy or dismantling the Papal States, not in the least because they were not particularly sympathetic to the conservative clergy.

So thanks to of the Napoleonic roots of the Italian Unification movement, the members of the Piedmontese (and later Italian) Parliament had very few misgivings about taking Rome; indeed, it was seen as the vital last step in creating an Italian State. However, the conquest of Rome opened up a whole bunch of cans of worms. The Pope excommunicated the House of Savoy, and in much of Italy (especially in the south) lack of cooperation from the clergy was one of many obstacles in establishing an effectively run state. Although there were a number of complex factors at work, the Papacy's unwillingness to recognize the new Italy certainly contributed to the small but protracted insurgency in Southern Italy. Further, a whole contingent of the Roman Nobility followed the Pope in his refusal to acknowledge the Italian State; they would come to be called, "The Black Nobility." Until the Lateran Pacts of 1929, the continued Papal refusal to recognize the Italian state would be a thorn in the side of the Kingdom of Italy and a small but not insignificant contributor to instability and delegitimization of unified rule in the Peninsula.

I had gone into detail on the characteristics of restoration-era Italian states here.

If you're interested in 19th century Italy, these are great resources:

Davis, John A., Italy in the Nineteenth Century, 1796-1900. Oxford: Oxford UP, 2000.

And these Italian-language sources:

Romani, Mario. Storia Economica d’Italia nel secolo XIX. Bologna, Italy: Il Mulino. 1983.

Negri-Zamagni, Vera. La situazione economica e sociale nel meridione negli anni dell’unificazione: Una rivisitazione.” Meridiana. 73.74 (2012). Print.