It shouldn't, I just recently switched from a Samsung Captivate to the Moto Atrix, but I had been using a BB charger with the Captivate for months. You can thank the European Union for cell phones going to the micro USB for charging. The EU required cell phone manufacturers to settle on a standard for charging accessories and that was the micro USB.
BTW, I have used the BB charger with the Atrix and had not had any ill effects from it.