Considering that Queen Victoria had set up Torchwood to protect earth and the British Empire from aliens, including himself, the Doctor wasn’t surprised that the organisation’s charter was largely a polemic aimed at him. It effectively named him public enemy number one, despite the fact that he was dedicated to protecting the planet from aliens who really were a threat. He couldn’t help thinking Her Majesty had overreacted, just a bit.
Still, that little misunderstanding wasn’t going to deter him from coming to the rescue whenever earth needed him. If Torchwood wanted to capture him, they were welcome to try.