Just as Job is the athiest's Bible book of choice, Francis of Assisi is their saint. Of course, this isn't because the fictional character of Job or the real Italian monk shared a disbelief in God. St. Francis was very much a devout Catholic, going so far as to allegedly receive stigmata. But the form his beliefs took in his daily practice shared a great deal with humanism - care for the poor, love of nature, a dedication to poverty that would later be co-opted by anti-capitalist movements. Like most Catholic historical figures (and saints in particular) his real-life zeal mainly focused on conversion and preaching the gospel (I don't mean this in a negative way - if I believed in a god I'd probably want everyone on board, too). But as is so often the case this has fallen by the wayside in retrospect, and what is left is the grand side of Christianity - quite simply the teachings of Jesus, particularly on the social issues.
This is where The Flowers of St. Francis resides. Roberto Rossellini's film is more a meditation than a narrative, a series of vignettes that have no specific destination and are only connected by the recurring characters, particularly Francis himself and a young disciple named Ginepro. As a result, your reaction to the finished product will largely be a result of how you choose to interact with the teachings of Francis and how that compares to Rossellini's understated and gentle presentation. Personally, I don't entirely feel qualified to review the film - Christianity is kind of like opera for me - so I'll just say I think The Flowers of St. Francis gives you a pretty good idea of where the saint was coming from, or at least where Rossellini thought he was. For a heathen like me, that makes it more of a picture of Italy post-WWII and the humanist aesthetics of neo-realism married to the Catholicism that remains infused in Italian culture today - making it a nice companion piece to Rossellini's war trilogy.