Of course, tents are inherently wind-vulnerable. After all, they're no more than light fabric stretched over a frame of aluminum poles. The tent canopy usually fits pretty snugly, but the fly can be a problem. Plus, a three-person tent is larger than a two-person (well, duhB), so presents a bigger target= for the wind.
Marmot's The Loft 3P ($349; www.marmot.com) is a three-person tent with excellent ventilation and vestibules that have a support pole, which should help stabilize the tent. Same for Mountain Hardwear's Hammerhead 3 ($295; www.mountainhardwear.com). I also like Sierra Designs' new Super Nova ($369; www.sierradesigns.com), a sturdy three-person tent.
That said, any tent will flap some in high winds. Setup will make a big difference. Invest in a half-dozen small nylon bags (about the size of a bread bag) and some strong cord. At the campsite, fill the bags with sand, attach the cords to the bag and to the tent's guy-out points, and bury the bags with the cord pulled taut. That will be of considerable help in stabilizing the tent. Also take pains to ensure that the tent is set on ground that's as level as you can make it. One twist in the tent frame will cause some parts of the fabric cover to hang loosely, increasing their tendency to flap.