Large bridges over the Rhine have existed since 55, when Caesar built a massive timber bridge in only ten days and marched his army across. A couple years later he built a second bridge. Crossing in boats is perfectly possible, Caesar mentions the possibility as one of his options, but decided that a bridge was safer. The Romans built dozens of bridges across the Rhine during its time as the limes, and these bridges are still preserved all along the course of the river--and there would have been under the Principate and into the Middle Ages many more temporary wooden bridges, which would have either been taken down (like Caesar's) at the end of a campaign or simply haven't survived. People in 1550 were perfectly capable of building bridges, this is at the tail end of the Gothic Period--people who can build structures like Notre Dame cathedral are well able to build bridges. Ferries are even easier. The OCD notes that the modern Rhine, with its many canals and dredgings, is narrower and deeper than the ancient (and presumably medieval) river. The OCD points out in particular that in antiquity the river was much more likely to freeze in winter, because of its much shallower depth--famously on December 31, 406 the Vandals crossed the frozen river. There was no particular problem crossing the Rhine in 1550, particularly somewhere as far upriver as Heidelberg