You can hardly claim in all seriousness that the Roman Catholic Church controlled Europe. In the right hands it could possess a formidable amount of religious and political clout, but this does not constitute the same thing as control, and indeed in the right hands a state could survive and even thrive despite the Papacy’s wrath. Certainly (in but one example) the inhabitants of the Holy Roman Empire during the reign’s of both Frederick I Barbarossa and his grandson Frederick II would be surprised to hear that the Roman pontiff enjoyed much control over the Reich.
But more importantly, the Roman Church was responsible not only for preserving and collecting books (as you rightly say), but also for making these works accessible to a larger audience. Secular aristocrats, middle-class burghers and lay clerks (to name but a few non-ecclesiastical sections of society - more on that later) often prided themselves on their literacy and their skills were highly sought after and prized.
Actually, this is the era when we first see the rise of systematized education. Indeed, the first universities like those of Bologna, Paris, Oxford, Salerno, Montpellier and Padua all emerged in this era and ensured the spread of knowledge far beyond anything that had been seen in the days of the Roman empire. Likewise, smaller grammar schools (often attached to parishes) helped contribute to a growing literate middle-class. Again, its not nearly so expansive as the reach of education is these days, but it was a whole lot bigger than anything that had existed in the Roman empire.
Books were certainly harder to manufacture in the days before the printing press, yet that hardly justifies this sweeping generalization. Not all books were massively thick and carefully illuminated tomes; such expensive projects were indeed difficult to create and a comparative rarity, but they are hardly representative of the majority of books produced during the period. Knights frequently read (and even composed) books on subjects like combat, horsemanship, hunting and poetry, whilst masons and other engineers had to be familiar with the geometry of Euclid, which was essential knowledge for designing everything from castles to Gothic cathedrals to siege engines; navigators the geography of Ptolemy; clerks, mathematics and philosophy; doctors, the medical works of Galen and Hippocrates. Even poor, isolated hermits (such as the 12th century English hermitess Christina of Marykate) could often be found in possession of at the very least a psalter. Literacy and access to knowledge may not have been nearly as widespread as they are today, but they were certianly not the sole purview of the Church and it was a skill that was greatly valued in medieval society by both clergy and laymen.
The truly expensive and hard-to-get books were the massive and delicately illuminated Bibles. Such works were indeed incredibly time and resource consuming, but when completed they were the pride and joy of any collection. Those kept in the great cathedrals and monasteries were often put on public display on a special lectern where their beauty could be appreciated; after all, what point was there in going to such effort to create works of inspiring religious beauty if none could see them?
Eh, I’m guessing you’re thinking of the ban on Aristotle’s works of natural philosophy at the University of Paris in the 13th century, a ban which was short-lived and which had no authority beyond the confines of that single institution. Other, similar bans were occasionally enacted, but often had little effect and were often rescinded in short order. In general, however, the clerics of the Roman Catholic church was perfectly happy to translate and preserve the works of pagan philosophers and later Arabic commentators; after all, had not St. Augustine called such writings “the gold of the Egyptians”, something to be valued by Christians? Indeed, so highly valued were the works of Greek philosophers that it was not an uncommon sight to see them depicted prominently on the edifices of churches (see this portrait of Aristotle from Chartres Cathedral, for example: http://farm5.staticflickr.com/4110/5168047158_c900ae0429_o.jpg) The works of writers like William of Conches, Albertus Magnus, Thomas Aquinas, Duns Scotus, John de Sacrobosco (to name but a few) were all informed by the works of the ancient Greek philosophers and were widely read and discussed and nobody tried to ban their efforts to find a synthesis between the knowledge of the ancient philosophers and Christian theology. We should also consider that post-Reformation Protestants were every bit as capable of issuing indexes of banned books and repressing printing presses during tumultuous times; it is hardly fair to act as if such occurrences were solely a Catholic trait.