You've gotten a lot of good advice already, and I agree with what the other posters are saying. It is important that you get a handle on your fear and anxiety so that you can begin to help your son. I know it's not easy, and you haven't done anything wrong, so please don't feel bad :) Just make the decision to change how you feel and act about going to the doctor, and work towards that goal.
I also think it stinks to have a doctor with a bad bedside manner. I honestly don't know how these folks are able to keep patients acting how they do, especially kids! I hope that you can find one that better suits you and your son's needs. Until then, don't be afraid to speak up!
For the future, I like the idea about getting a toy doctor kit and playing/role playing to get him comfortable with the tools and what they're for. Also, if you get the Disney channel, there is a series called Doc McStuffins that is really cute about a little girl who "doctors" all her toys, and fixes them up when they get broken. The toy is always a little afraid of getting a check up and the girl and other toys help make them comfortable so the doctor can do her job and make them better. If you don't have cable, you might be able to find it online or maybe on DVD (not sure because it's pretty new).
For today, see if the doctor will allow you to do the exam with your son in your lap. When your son needs to lay down, sit knee to knee with the doctor and have your son lay across your laps. When it's time to look at the ears, hold your son cheek to cheek while the doc looks in one ear and then switch for the other ear. Having you close will hopefully help him to feel more calm. Also, try your hardest not to anticipate anxiety and practice slow, calm breathing and a relaxed posture so your son can mirror you.
And definitely, a stop at the ice cream shop afterward never hurts :)
Good luck!