I have a metal clip to hold money in my wallet (not that I ever have money in my wallet, another story) which sets off the walk throughs. I'm not saying your wallet would set it off, but lots of people's do.

I think they are just trying to get you through in one shot. Asking for wallets, watches, shoes, belts and the rest of the stuff they are asking you to remove (depending on airport) may keep you from beeping on the walk through, which means you will not have to be wanded, patted down, or start removing things and going through again and again.

I always put my wallet in the carry on or jacket pocket to go through security, way before all of this it would set the machines off. I was never comfortable putting it out in the open in a basket in the open.