I'm currently in Medellin and the protests here have died down (or at least we have not been aware of/inconvenienced by any demonstrations over the last 2 weeks).
We decided *not* to go to Bogota due to the protest/security situation, but that may have been an overreaction. You have to be security-conscious in Bogota in normal times...this is just a new thing to stay attuned to.