There are a couple of ways to think about this. First, considering your atom economy equation. Typically a catalyst is used in place of a stoichiometric reagent. A catalyst is (strictly speaking) not a reagent, so it's effect on the atom economy is neutral. The alternative stoichiometric reagent is a reactant, so it will reduce the atom economy. This leads to the conclusion that a catalytic method offers better atom economy than an alternative, non-catalytic method.
From a slightly different point of view, atom economy is one aspect of measuring the amount of waste that comes out of a reaction. A more relevant quantity is really the ratio of the mass of the desired product(s) to the total mass of all of the reaction inputs (including reactants, catalysts, solvents, purification materials, etc). Since catalysts can be used in smaller amounts than stoichiometric reagents, there will physically be less mass put into the process, which increases that ratio.