Was it ever the case that one fine spring day in 1325, Jervis the plowman just up and thought to himself, "hey, this whole thing is bullshit!" Or would that have been inconceivable? Such a sentiment gets you an eyeroll and a tip of the fedora on Reddit, so common and banal that it is, but back then was it even possible for the average schlub, let alone scholars and bishops, to just have a full-on epiphany of disbelief?
Were their any scholars that managed to do so prior to the Renaissance (thinking of Giordano Bruno, for example)?
Or were your only options a) Rome; b) some heretical Christianity-based sect such as the Cathars; c) Islam, if the Turks came knocking; d) some form of occultism that wouldn't have gone so far as to swear off Christianity like today's neo-pagans do; e) ?.
From what I can tell, the Church enjoyed all but unchallenged ideological hegemony over everyone from king to beggar, the only competition coming from heretical sects such as the Cathars, hedge witches selling love potions to horny peasant lads, uppity local bishops and princes bucking under the yoke of Rome (who would never think to deny Christianity itself), and Islam.
I hope this question is not too broad or vague. I've been pondering it for a while.
No.
First, to clarify, there were no Cathars after the early 14th century.
With respect to total non-belief, there was a thread on atheism in the middle ages a while back, and the upshot of it was that the only major figure that can tentatively be identified as atheistic is HRE Fredrick II. Even with him, it is hard to tell polemic from fact. Whether or not there was private non-belief is an open question, but my own feeling, developed from my research, is that there is a non-negligible number of what we might term "non-practicing Catholics" today. This comes with the caveat that yearly communion was required for all Catholics by Lateran IV in 1215, but still, that seems like a fairly superficial requirement for devotion.
That said, I would categorically reject the idea that just because people operated within the bounds of the institutional Church meant that the Church enjoyed an ideological hegemony. First, this implies a degree of control which simply did not exist. Second, it would ignore the abundance of diverse religious practices and groups that exploded across the face of high to late medieval Europe: the Cistercians, Praemonstratensians, Beguines and Beghards, Waldensians, Dominicans, Franciscans, Lollards, Humiliati, Hussites, to name a few, all constituted a distinct (if occasionally heretical) abundance of unique expressions of devotion. This was mirrored by the growth or invention of new cults and centers of worship. Marian devotion took off in this latter period, and the cult of the Holy Wounds became massively popular. Even the much-maligned schools with their medieval theologians counting angels on the head of a pin contained many unique forms and expressions of devotion.
Working within the rough boundaries of the Church, or even somewhat outside them, the age had a deep and profound piety which manifested in a startling number of ways. I would close with the reminder that the Reformation was not, in point of fact, about religious freedom, at least not at first. It was a criticism of the Church as insufficiently devout, and of empty expressions of piety. It sought reform, not overthrow.