ThatGirl - you're right. However, what to do about it is the $25,000 pyramid question.
Generally, in business, intellect means nothing if it's not profitable. There are two types of people who are higher up on the food chain. Those that realize that having intelligent, free-thinking people working for them will ultimately lead to greater profits if they can manage them effectively, and those that are not smart enough, or not effective enough at leadership, to want those kinds of people under them because they know they do not have the skills to direct them to create greater profits.
I have known quite a few very intelligent free thinkers in various jobs who had various positions, and their intellect and free-thinking had nothing to do with how much money they were able to make the company. Ultimately, this is all that matters in business. (Taking into account things which are ultimately profitable, but not necessarily immediately recognizable on a balance sheet, such as great customer service, unique design, a high-touch approach, etc.)
If you are currently in an organization, I think the best thing to do is to walk the fine line between shining and outshining. You want to make your work more efficient and effective, without outshining your boss. You want to make your boss look good. If your boss is not effective, you may be able to go over your boss' head and look good to your boss' boss, but beware this is a very dangerous road...