It seems like the CTA is attempting to make policy, without obviously violating laws. Areas without clear policies either require clarification by the elected officials, or should be left to individuals in the field. Unions and corporate lobby groups have no place in making policy.
Unions shaping policy is a very controversial subject, and I believe that there is no widespread consensus on whether it should or should not be permitted. It is one of the arguments made against public-sector unions, in that they have an improper influence on government policy, and thus undermine the democratic process.
I thought unions existed to collectively bargain for compensation and working conditions. When working conditions are related to policy, they can negotiate with the employer for 'concessions' (or agreements as the case may be). One (potential) problem occurs when the politicians and the unions agree on something, and enter into contracts with the purpose of 'locking-in' policy decisions beyond the politicians' terms.
In the case of workplace conditions and such, sure. But there's a huge issue of moral hazard when it comes to unions lobbying or influencing public policy more generally for their own benefit, for example with prison guard unions opposing the legalization of marijuana. Locking people in cages for the sale of a relatively harmless plant might benefit the prison guards, but that benefit is vastly outweighed by the harm to society.