I imagine that by saying you are "too polite", your boss is trying to nicely explain that you do not project the confidence and authority you need to get clients, coworkers, etc to respect you and listen to you. While I don't want to pretend what kind of events are leading him to say this to you specifically, some examples might be saying "Would you mind doing this for me and can you tell me how long it will take you." when you really should be saying "do this by 5pm today". In business, sometimes, we have to be tougher and more direct than maybe what we prefer to be in our social lives. In addition, you're often going to run into people who will buldoze you to get what they want. You have to be able to deal with those people and push back without worrying about how "politely" you might come accross. At the end of the day, it's a balancing act. You don't want to be rude, but you definitely need to direct, loud, and 'bossy.'
And yes, this is very true of the military. Even in peacetime operations, the military functions as it might on the 'battlefield', at least when it comes to working climate. While there has been a lot of improvement in how the lower ranks are treated and shown respect by their leaders, there's a lot more 'direct orders' than there are times when people are going to stop and make sure they haven't said anything that upset you.
I would talk to your boss and try to get some clarifications on what he's saying and some suggestions on what you can do to improve in his eyes. It might be that your ethics don't match his or the company you are working for, or it could just be that you need to learn how to project more authority.