I currently have (counts them) five contactless cards in my wallet, and the CSR was #5 ... you have a few options:

• Take it out. This is the obvious and foolproof, if less convenient, answer.
• Put them on different sides of your wallet. I have my local transit card on one side of the wallet and my other transit card and payment cards on the other. It's easy to tap in a way where the reader can only see the one card by itself. On a standard bifold wallet, put your hand between the halves.
• Chicago-specific, if you're paying with your own money just use your Chase card--you can add passes to contactless credit cards at the CTA vending machines now, and transfers finally work too. If you're using transit benefits or pre-tax deductions, nevermind this one.

You could join the ranks of the paranoid and buy an RFID-blocking wallet, but then you'll definitely have to take your card out.