Why do we learn Gemara, where each opinion gets equal weight and the strongest opinion wins, and we are thus taught not to be peti, but to only accept a true answer, while today, its enough that one Rabbi said 'this' and we don't bring arguments: if he said it, it's holy of holies. Why not ask questions and find the truth? Just like the Gemara, but today? An example we learn from the first daf of Maseches Horayos where if one who learned knows the halacha and the Sanhedrin was wrong, he should have not listened, but argued until they did a psak. Then he is a zaken mamre if he publicly contradicts the Sanhedrin's ruling, but he must stick to his opinion in private, for if not, then when the Sanhedrin finds they are wrong, he has no kapara from their korban
When the Amoraim Paskened, the people had to listen to them as well. What you are seeing is the conversation between the rabbis.
A side point: Between the arguments we seem to forget that most often, when a greater Amora was quoted, it was taken as a Psak and a proof and not naturally questioned. For example. when Rav Mori bar Rachel got a Psak, he didn't wait until he got convinced. When Shmuel was quoted that was the end of the conversation, not the beginning of the debate. Arguing on a Rebbe was the exception, not the rule.
Nothing changed in this regard. Many Rabbanim argue on their Rabbeim in certain instances.