The problems I have run into have been acting like I know more than I actually do. Our first accountant assumed I knew everything since I acted like I was making informed decisions, which led to some issues. He also made a few mistakes (not capitalizing on section 179 one year for example).
In regard to your question about why your misconception is common, no idea. Just a quick google shows lots of accurate descriptions of the benefits of an S-Corp. Maybe a misunderstanding with your accountants?
After moving to a larger (and much more expensive) accounting firm, and learning from our previous mistakes, I've had a much more pleasant time dealing with this stuff. It's all arcane and stupid when it comes down to it, but you have to learn it to effectively manage your tax burden. If you don't actively think about it you get absolutely screwed on occasion, as it affects everything about your business. And the mistakes get expensive as your revenue scales up.
This is getting totally tangential, but you can probably hardly imagine all the crazy rules regarding taxation in the case of a sales event. Operating as an S-Corp is fine and dandy, but creates an additional hurdle for getting investment and for sales. S-Corps can only be owned by individuals, so an acquisition or an investment means restructuring, but you are restructuring after a planned purchase, which says certain things about intent which makes the restructuring likely a taxable event in and of itself.
I strongly strongly strongly recommend talking to an experienced business lawyer, and having them recommend an experienced business tax planner. This isn't schemey tax avoidance stuff, this is fundamental planning so you don't get a surprise $200k bill at some point!