Just to clear up a misconception I've seen mentioned a few times, I'll point out that a mid- to high-pull recurve bow (say 70 pounds plus) hits with approximately the same force (by area) as a .45 ACP slug, at any reasonable tactical combat range.
Strong bows penetrate armor just as well as crossbows do; better, at point-blank ranges.
A crossbow's big advantage over the bow is the flat trajectory and stable firing platform, which translates into "Simple Weapon Proficiency."
As for suggestions to even things out, I'd do two things, separately or in combination:
(1) Up the damage for the crossbow, as several folks suggested. The easiest way to do this is to assume that all light crossbows hit with Strength 14, and all heavy crossbows hit with Strength 16. (You could also give a virtual Rapid Reload feat free to crossbow users with 14 or 16 Strength, respectively. That might be too much; I dunno. The thing folks -- including me -- tend to forget when they worry about high-Strength archers is that those archers are only using half of their Strength bonus (the damage half), which is a pretty major balancing factor right there.)
(2) Recognize the immense amount of training that is required to use a bow effectively -- especially a powerful bow -- by requiring another proficiency. Maybe just do it for mighty bows. That'll even things out nicely with other missile weapons, but might screw too much with the balance with melee in your game.