The Southern Question is a rather consistent element of Italian politics following unification in 1861 and one which premises an assumption of political, cultural and/or economic backwardness in the Mezzogiorno. The economic and political issues likely have more substance than the cultural and these issues generally stem from the unitary government's interests being secured predominately in the North. There is, to be very frank, a great deal to be said about this question but in the interests of addressing elements of it in good faith, I want to reword your question to be a bit more charitable for the South: Why has Southern Italy struggled with the modernizing projects that are generally more common in other nineteenth century European nation states, i.e. industrialization, infrastructure development, and urbanization?

I should note that before we begin -- the general assumption of backwardness which is levied against the South could have been made in any region of Italy at the moment of unification. The notable exception being the Kingdom of Sardinia which had a slightly larger middle class and had generally taken inspiration from British liberal journalism and agriculture and had seen an increase in agricultural technology and something closer to 'modern' political discourse in the years before the Risorgimento. Even neighboring Veneto (the central city of which is Venice) had a pretty broad swathe of liberals and reformers who felt the region was backwards, most significantly affected by economic downturn that had started with Austrian annexation and continued to grow worse as Venice, once a celebrated world port, was increasingly irrelevant in the context of global trade. Figures like Alessandro Rossi, a wool magnate and Venetian industrialist in the city of Vicenza, worked to 'modernize' Veneto by industrializing textile production but struggled not infrequently with getting his workers to better follow the moral 'benefits' of modern civil society. This mostly boiled down to his frustration that his workers were less than willing to follow Rossi's intense Catholicism and were unwilling to save what meager earnings they made and instead opting to spend it on wine. Other liberal reformers of Veneto like Luigi Luzzatti, who would eventually be one of Italy's prime minister dedicated his life collective savings banks in Veneto to get workers to combat poverty by taking their money and investing it in the bank and not on...well: food and wine. I make this tangent to highlight that the question of, as you say, "historically lagging behind" is one that is often asked of the South but was in every corner in Italy throughout the nineteenth and early twentieth century and it is a genuine disservice to the South to pretend that this is purely a phenomenon of the South.

As for the legacy of the Southern Question, I can at least address an element of where it came from: the Brigand's War. I expound a bit on this in an answer here. Suffice it to say that the Bourbon regime, an absolutist government, was labeled by the unitary government as backwards and even suggested that the Kingdom of the Tow Sicilies was essentially a feudal demesne. This is not entirely incorrect, as the social elites who ruled throughout the Mezzogiorno benefited from the absolutists state and stood to lose their privileges by the new liberal Italian state in 1861 when Garibaldi's expedition overthrew the kingdom. That said, broadly speaking the 'brigands' who were fighting in the period of instability in the region were of a wide variety of political and ideological interests, a not insignificant portion of these factions was essentially paid by local Southern elites to vie for positions in the new administration. The line between crime and politics in the period following the Italian government's military occupation of the South was, to say the least, difficult to ascertain. The reputation of the south in both the Italian government and in many presses was that the region was beset by unruly upstarts but the vast majority of the violence as we understand it now came from competing southern elites and a terroristic crackdown on political dissent by the Italian government against everyone from Bourbon insurgents to Garibaldian republicans, all labeled as brigands.

There is a lot more that could be said about the racial discourse that had come from this, with figures like Cesare Lombroso and Alfredo Niceforo using bad statistics and race science to functionally racialize Southerners as mentally and physically inferior to Northerners. I'm not really going to dwell on it here because it is bad science but I will mention that the social and cultural legacy of the Southern Question did have such intellectual ramifications. In questioning why the South has struggled economically as opposed to the, admittedly rather modest, industrial achievements of the North, there are many thinkers who have tackled this question. Gramsci comes to mind. La Questione Meridionale, Gramci's writings on this subject broadly connect the cultural and intellectual othering of the South as manifestations of Northern investments which exploited Southern laborers, who no doubt suffered under the agricultural social order in the South. Essentially Gramsci argued that the South had been colonized and exploited by Northern monied interests which landowners in the South were happy to maintain. This argument has become pretty common within the context of the nineteenth and early twentieth century, though it does have limits.

For my money, though, the real economic issues which plagued rural Italy in a broad way was simply a staggering loss of young men to emigration in the nineteenth and twentieth century. While we generally think of Southern Italian's moving to the Americas in the twentieth century, it should be noted that starting with the Great Depression of 1873, severe contractions in global agricultural markets brutally damaged Italy's agricultural sectors and prompted tens of thousands of young men every year to seek work elsewhere in Europe and eventually the Americas. The first wave (1873-1890) was almost entirely Northern workers who, if they stayed, would have subsisted on meager rations of polenta which could lead to severe health issues like pellagra. By the turn of the century, Southerners began to move in even larger numbers as common rations included a couple pieces of wheat bread with some olive oil. Most these peasants, North and South, would have only had access to meat when they hunted for it, a rarer and rarer proposition as peasant land decreased as new land sales from the Italian government closed off more land in elite estates, or when it was offered for a Church service -- usually Christmas or Easter. The effect this emigration had on the Italian economy was, as you can probably imagine, very serious. While some workers returned after saving some of their wages abroad, many did not and the general population in places like Sicily were generally on the decline.

Of course, for those who stayed the gulf between North and South were still legitimate and reinforced by the continued politicization of the Southern Question. Social reformists like Giolitti did little to address the serious issues of poverty in the South, indeed cracking down on strikes and protests in much the same manner as the moderates and liberals who proceeded him. Among the feathers in his metaphorical cap, Mussolini claimed to have ended the Southern Question, which he did not. A good source if you are interested in both the limits of the Italian state, fascist or otherwise, and the particulars of everyday life in the Mezzogiorno in the midst of Mussolini's regime is Carlo Levi's Christ Stopped at Eboli, which essentially documents that Southerner's were aware of the political reality of larger Italy, but that, generally speaking, none of that mattered as much as local concerns of surviving. The title is an implication that even the Catholic Church had never really succeeded in penetrating the territory of a small town in Solerno. It's hyperbole, but only just.

There is much more that could be said about the so called "Miracle" of the twentieth century that saw the Italian economy lurch forward following the second World War, but that is not my area of expertise and thus I will stay in my lane. But to sum up some of my points, I would note that the problems faced by the Mezzogiorno were common in many areas of Italy. Lingering cultural and social assumptions remain but it is not entirely accurate to think of the South as functionally one step 'behind' a more enlightened North. In truth, the South was repeatedly put in a bad position by the previous Bourbon monarchy, the Italian state and the eventuality of connected global trade. While I will agree that these crises are serious and that on the whole the South was more effected that some other northern regions, I think that most historians would agree that these crises affected all of Italy and that the difference between North and South in questions of backwardness has been significantly overstated.

I hope this is helpful.

Edit: Slight correction on the name of Alessanrdo Rossi, the Venetian wool industrialist, which I had erroneously written as Adolfo Rossi, a prominent Italian journalist of the period. Oops.