The problem with your example is context. OP's link to the flat design is lumping all the UI elements together. Essentially, out of context. Even your use of the label was awkward. "Danger Button", the text, is weird. However, if you'd relabeled it Submit, or some other common action word, it would make more sense.

Couple that with the lack of a form.

I'm not saying that flat buttons are superior, or that 3d looking buttons are worse. Simply pointing out that context matters, and even your opinion is worthless. That it looks like a warning message to you is indicative of other problems, not merely the lack of 3d.