The only concern I have is that the content that happens to match markdown rules will get interpreted and the subsequent highlighting etc might surprise/annoy a user not familiar with markdown. E.g. adding a dash at the beginning of the line will get interpreted as a list item, typing asterisk will trigger the editor to put another asterisk and put the cursor in the middle with the expectation that you want to type bold text - you can press backspace to remove the extra asterisk and continue as per normal but if you are in the business of dealing with loads of asterisks/dashes at the beginning of the line, and don't care about markdown, you might be pissed.
All the approaches to handle this kind of thing are not as simple as turning off a checkbox. If that is a deal breaker, then this may not be the app for you. OTOH, if you don't mind occasionally dealing with that (or better still, picking up the bare minimum amount of markdown), it'll provide a pretty rich note taking experience. For typical content, I don't think this will be a frequent issue but then again, what is typical for someone may be atypical for me and vice versa.
Personally I think it is totally worth it but YMMV.