The city has been exacting the “voluntary’’ PILOT payments from non-profits for quite a while, with the big universities and the hospitals bearing the brunt of Mayor Tom Menino’s tough love. The rationale isn’t hard to understand. Boston delivers services, such as fire and police protection, and street maintenance, to the non-profits for free. As charities, they are exempt from city and state taxes. Boston has less dough than ever, so it has been jacking up the PILOT payments accordingly.