The pressure difference actually is taken into account in the equation. The pressure in the fluid immediately below the meniscus is less than atmospheric. So the atmospheric pressure pushing down on the fluid in the bath forces fluid up the capillary. It's like sucking on a straw. If you combine the Laplace relationship with the hydrostatic balance on the fluid, the atmospheric pressures cancel, and you are left with the Lucas Washburn equation, sans the acceleration term and the viscous term.
Chet