That does end after a while (the headaches, typical withdrawal symptoms). Maybe it's the age, but I found that my caffeine tolerance went down considerably after age 40. I found that it would keep me up at night and actually started having some anxiety issues as well - namely unexplained heart palpitations, shortness of breath. Cutting caffeine down by drinking only decaf coffee or herbal teas helped dramatically. Yes, I had some headaches as I started down the decaf path, but after a few weeks, those subsided.
Yes, I know that decaf isn't necessarily good for me either, but I still love the taste of coffee and my brain still believes that it is waking up from the coffee. Go figure.