The weak phytoestrogens in flax seed apparently fit the cellular estrogen receptors without activating them. Having the weak phytoestrogen attached to the estrogen receptors may prevent strong estrogens from activating those same receptors. Eating flax seed meal might prevent some of the problems supposedly associated with coffee estrogen.
It might make sense to eat som flax meal before drinking coffee, so that some of the weak phytoestrogen is already attached to the receptors before they are exposed to the strong ones.