In the 201st year of the 4th Era in Skyrim, there is a lot of mixed responses to magic. Certain types of magic, like Restoration, seem to be pretty commonly accepted, as it is practised by priests and the generic guard dialogue is very positive to the school. Summoning undead is, by all accounts, frowned upon, though this is true of many other places in Tamriel as well. For example, it being done by others than the Tribunal Temple in Morrowind towards the end of the 3rd Era is not cool with the Dunmer.
Why is this? Is it simply because the Nords "don't like 'em mages"? As best as I can tell, the distrust for magic in Skyrim is a recent historical phenomenon and has to be understood in the historical context. Onmund, a Nord innitiate at the College of Winterhold, will give a few reasons: 1) Nords don't trust magic "in general", 2) the Oblivion Crisis being made possible by mages, 3) the collapse at Winterhold and 4) the war with the Dominion, who are "magic users". The first reason seems unlikely, given the lack of distrust towards magic in general the Nords show prior to Skyrim, and is probably a result of the 3 other reasons. All of which are developments that occured over the last 200 years.
Something else that changed over the last 200 years is that the Mages Guild, the only institution whose purpose is to make magic accessible to the general public, has fallen apart. The Synod and the College of Whispers emerged from its ashes, but what little we get to know of them suggest that they are more political organizations for mages, rather than a mage organization for learning. J'Zhargo, everyone's second favorite housecat, seem to suggest that the College of Winterhold is one of few places left dedicated to studying magic for its own sake. And the College of Winterhold, while not really that opposed to dealing with the general public, is a single college in one of the Old Holds in Skyrim. As opposed to the Mages Guild, who had guild halls in nearly every major city in Tamriel. Another thing that happened is that the Psijic Order left Tamriel for the time being, due to something related to the Thalmor in Summerset Isles.
Why does this matter? Well, the simple rule to follow is that people tend to distrust things they have no grasp of. Prior to the Mages Guild, the mages were usually not just anyone. Witch Covens, Shallidor's stuff, the Psijics, the Nibenese magistocracy, the Telvanni, all are quite isolationist and it is likely to say they were distrusted as well, to some extent.
Maybe I am stating the obvious here, but I think it is far more likely that the distrust we see in Skyrim towards magic is a result of the collapse of the Mages Guild more than anything, and is probably not all that uncommon when it comes to commoners from all over Tamriel.