Ruhollah Khomeini, the Founder of The Republic of Iran and Ali Khamenei, the current Supreme Leader were both critical in the forming of Modern Iran, but they got and maintained their power in very different ways.
The now-deceased former Supreme Leader and founder of The Republic of Iran, Ruhollah Khomeini, was a leading participant in the Iranian Revolution of 1979. Khomeini was immensely popular and seen as a Hero by those who soon became his people. It's really hard to express just how intensely Iranians loved him in simple terms. His return from exile, which closely coincided with the fall of the last Shah, saw crowds of more than 5 million; more than the largest concert in human history attracted: Rod Stewart at Rio de Janeiro's Copacabana Beach on New Year's Eve 1994. It is worth noting that the ~4.2 million members in attendance of the concert were also treated to fireworks later in the evening. Khomeini's funeral drew a crowd of 10 million, twice the size of the Cubs 2016 world series parade (Comparing the infrastructure of 1989 Tehran to that of 2016 Chicago makes you wonder how a gathering of that size was even possible). After the burial went awry, the body was loaded back onto a military helicopter (pictured above), but as they tried to take off, people dragged the helicopter back down. These were not fake mourners who were forced to cry for hours until they passed out from dehydration, as was the case with North Korea's Kim Il-sung (Demick, Northing to Envy, 2009); these were real people mourning the loss of their beloved leader. This truly underscores the cult of personality that he built up and points to his charismatic legitimacy.
When discussing legitimacy, we typically observe its roots in some form of social contract. Tilly, who defines the state as "relatively centralized, differentiated organizations the officials of which more or less successfully claim control over the chief concentrated means of violence," believes that this social contract is not an ideal way to understand states and their formation. He argues that leaders, especially those who actually formed "the state" themselves, are "coercive self-seeking entrepreneurs." Tilly defines legitimacy as "the probability that other authorities will act to confirm the decision of a given authority," (Tilly, 1985) which is similar to O'Neil's definition, is absolutely critical, especially in non-democracies or otherwise unstable states where we might find factions competing for legitimacy.
Khomeini used his charismatic legitimacy to his advantage and consolidated power for himself instead of in state institutions from his induction as Supreme Leader even past his death. Khomeini's will "explicitly asked the military to stay out of factional politics, warning, 'The revolution belongs to all the nation.' Even Khamenei, who has embraced the IRGC much more closely, has stressed the same message." While Khomeini requested that this despotic power not be used, Khamenei has obliged "forb[idding] military, security, and intelligence forces from intervening in elections" (Vatanka et al.) but has still managed to keep a firm grip on his state.
Sidney Tarrow, in "War, States, and Movements: With Tilly; Beyond Tilly," focuses primarily on the state in wartime, but the Islamic Republic of Iran has been in almost constant conflict since its founding (Iran-Iraq war, nuclear program related diplomacy issues, and several more recent wars against the Islamic State (ISIS) in multiple countries) so it most certainly applies to Iran. Tarrow references Micheal Mann's definition of infrastructural power: "the power of the elite to penetrate and centrally coordinate the activities of civil society through its own infrastructure," which we can contrast with a despotic state which "crushes opposition and regards civil society as a territory to be conquered." (Tarrow, 2014)
Khamenei has done this through the use of infrastructural power, which has helped him remain in power (despite not being seen as the hero of the revolution like Khomeini) because "a state built on infrastructural power and rule by law also has the flexibility to create new ways of achieving its aims." (Tarrow, 2014). Part of maintaining that flexibility, however, is offering concessions when grievances or demonstrations occur as meting them with force would only damage the institutions applying that force as the line between "behind the scenes" infrastructural power would be crossed in showcasing despotic power. Similarly, Gandhi and Przeworski note that those who cross this line in non-democracies do not hold power long primarily because civil society does not like despotic power and because its use weakens institutions and increases the demands of civil society. As Gandhi and Przeworski mention, Said demands may also serve to weaken institutions. That is why, in terms of remaining in power, the following is best: "policy compromises entail an institutional setting, typically legislatures. The degree to which assemblies are organized along partisan lines in turn influences the extent to which authoritarian rulers must make compromises. If rulers counter the threat with an adequate degree of institutionalization, they survive in power. (Gandhi, Przeworski). Many of these concessions came during the presidency of a reformer (whom he opposed as a conservative), the election of which could also be seen as a concession. "The need for cooperation depends on the existence of ready-made institutions capable of organizing rule" (Gandhi and Przeworski, 2007), and at the beginning of his rule, Khamenei did not have sufficient institutions to wield as someone without charismatic legitimacy comparable to Ruhollah Khomeini, but he built them up over decades and has firmly cemented his place in Iran. The reasoning behind that is solid; Khamenei invested in institutions building because that is what he had to do to survive, but according to Benjamin Smith in "Life of the Party: The Origins of Regime Breakdown and Persistence under Single-Party Rule," this is quite common as those "who face and survive the most strenuous fiscal and political crises early on are likely to do so because they have invested heavily in institution and coalition building." (Smith, 2005).
Today, Iran's clergymen are under attack by many from inside and outside Iran. Many point to human rights violations and economic turbulence as key reasons for the current regime to be eliminated and for a new, wholly democratic system to rise in its place. These individuals have long been barred from running for office, especially that of the president. Preventing candidates from running for office is one way to silence opposition without using force (or despotic power). The institution most effectively used by Khamenei is the Guardian Council. The group wholly controls which candidates are allowed to run for office and reviews everything passed by the popularly elected parliament. The Council has also done a great deal to increase the influence of the IRGC, which Khamenei commands outside the bounds of the constitution, and thus all forms of government oversight.