Originally posted by crooktooth
The medieval universities were considered religious institutions, and were under the jurisdiction of clerical law. Most law studies on offer were in canon law, the law of the Church.
Of course, the studium generale(what "universities" were called in the high middle ages) could be a exclusively religious institution, but more often as not(as in Bologna) it was run by a council of students, or(As Paris or Oxford) by a guild of instructors. Usually, the larger universities existed under they're own set of codes and laws, usually based on canon law but set apart from it in agreement witht the city in which it resided. The older schools were indeed based in monastries, but in the flowering of the studium generale(13th century), most of them, though usually centered around a cathedral(excepting italian municipal schools, based in the individual city-states), were not overly more more religous than the rest of medieval society. (which, as you've already correctly remarked, in out eyes would seem very religious). Indeed, the SG held close ties to the intellectuals in the church (the students in Paris were summoned to studies by the tolling of the bells of the Notre Dame, a great many of the teachers were churchmen), but this was only to be expected since it grew out of the older tradition of schools. This intermingling of the church in the learning institutions would carry on for several hundred years after the renaissance, and in many cases continues today.
However, to state that canon law was the sole focus of law studies is a gross overexaggaration. "Roman" law was studied extensively from the late 12th century onwards, and secular(that is, not _within_ the church) careers in medicine were also possible.
Religious dissent was very common thorough the middle ages, but I presume you mean objections against the church from grounds of reason or atheistic views. This was not something the italian renaissance brought. *Renaissance Humanism concisted of an increased emphasis on the humanities, that is, classical languages and literature, precise expression, historical scholarship, and the arts*(sic Hollister,1994). The renaissance humanists looked to the older classical ideas and the classical culture as a whole, rather than as a set of ideas one might use. In this they were different from the older scholars. They did not, as a whole, reject religion and indeed retained a great many "medieval" characteristics. Savaronala was a child of the renaissance as much as Da Vinci.
When it comes to the ideas of reason, opposing views on religion, and the beginning growth of secular literature, that is something that came solidly from the middle ages. Peter Abelard, Hildegard of Bingen, Robert Grosseteste, Roger Bacon and William of Ockham were medieval thinkers, rationalists, and in some cases, as Ockham, proponents of the idea that the study of God must be based on faith alone and the study of the natural world must be based on observation.
Villon, Chaucer and Christine de Pisan all wrote "secular" literature in the pre-renaissance period. All these people were firmly religious, just as the renaissance thinkers were. Reason and religion did not seriously come into conflict before the 17th century.
EF