That it was what the people wanted via their Congressional representation and that SCOTUS would stop the nonsense before it went into effect. Bad choice. At least, that's my assessment of why GWB signed CFR.
My take on it, for what it's worth, is GWB wanted McCain's support on other issues such as the wars in Afghanistan and Iraq. So he signed CFR while expecting the SCOTUS to strike it down, but incredibly, it was upheld.