This is a question that medievalists often struggle with because of the widespread and diverse nature of popular heresy and dissent in the 11th - 13th centuries (a very general timeframe, mind you). The best answer I can give is that St. Francis was seen, though still an itinerant preacher focused on imitating apostolic poverty, as more in line with the Catholic Church and its views on orthodoxy. Lateran Council IV in 1215 focused solely on consolidating the Church's authority in areas concerning the clergy and related bodies (formation of Orders) and the construction of orthodoxy, in many ways inspired by the earlier Gregorian reforms, by which to manage the many emerging mendicant groups of the time. Thomas of Celane's "Life of St. Francis" (1228) goes to great lengths to show that Francis was symbolically folded into the Church (especially following his ordination that allowed him to preach under Church authority) and constantly reaffirmed by the Church after instances in which he edged too far out of Church authority. Of course, where those boundaries lay and how transgressions concerning them are dealt with are what cause Francis' exception to provoke disagreement.

Overall, I think R. I. Moore describes the overall situation of popular heresy and dissent in western Europe during the eleventh and twelfth centuries quite succinctly: "That Robert of Arbrissel, Bernard of Clairvaux, and Francis of Assisi were revered as heroes of the church whose faithful fell over themselves to provide for their followers, while Henry of Lausanne, Arnold of Brescia and Valdès were reviled as the emissaries of Anti-Christ and their disciples hounded and hunted to be visited with increasingly savage penalties, argues either a singular arbitrariness on the part of the church or the existence of some source of division more profound than the niceties of religious doctrine ... Christian niceties of doctrine were important, that Christianity 'has always been concerned with right beliefs as well as right conduct, [that] the Christians' interest in abstract truth led them to try to define it in a system of orthodoxy, and since no definition of truth ever goes unchallenged, the inevitable companion of orthodoxy is dissent ... Heresy was only an approximate criterion of dissent, and does not wholly explain either its incidence or its reception" (Moore, p. 265).

Sources: Thomas of Celane, "Life of St. Francis". 1228.

Moore, R. I. The Origins of European Dissent. New York: St. Martin's Press, 1977.

And for an examination of the early Dominican Order and how it came to be accepted and utilized under the Church, I recommend:

Ames, Christine Caldwell. Righteous Persecution: Inquisition, Dominicans, and Christianity in the Middle Ages. Philadelphia: University of Pennsylvania Press, 2009.