I kind of always suspected that the ponies in Ponyville suspect something wasn't right with the Mane 6 (except Twilight of course). But because Equestria has faced many threats (I know Ponyville gets this, but I suspect it's the same in other places), they decided to go along hoping somehow everything will get fixed. I only suspect that because of the Slice of Life episode, where the ponies were't too bothered by a Bug Bear monster but more worried about Cranky and Matilda's wedding (well not that worried but still).