To clear bumps of any size and to stay in control, the tires have to keep rolling. Let your wheels roll over roots and rocks, so that all of your traction is available for steering and slide control. Rather than wasting your traction on the roots with heavy braking, try to do your speed control on the non-rooty parts between obstacles. To do this, keep track of where your wheels are, and keep a feather touch on your brakes, ready to grab a handful of them when the opportunity arises. You'll be able to slow much more effectively on solid ground, and you'll have more control.
Road more about mountain bike braking technique, like about why you shouldn't drag your rear wheel.
Soak up the Bumps
Especially when moving quickly, a plush suspension fork is a great help in handling the lumps that trails throw at you. When you're moving less quickly, or riding a stiffer fork, your body must act as a useful suspension. Many riders will stiffen up when presented with a rock garden or a network of slippery roots rushing up at them, but one must do the exact opposite.
Keep your arms bent and your butt off the saddle. Be supple and fluid, like a ballroom dancer, and let the bike hammer about below you as you gracefully float down the hill. Don't let the roots bounce you around -- keep your arms and legs loose to soak up the bumps.
Take Obstacles Head-On
Just as when hopping a curb, be sure to approach a root head-on. Especially when it's wet or muddy, or when riding big knobby tires with a low surface area, the front wheel can slide sideways along the root if the approach is not close to 90 degrees.
Keep the Tires Flat
Thinking about tire pressure? Think again. Sloping obstacles demand that you keep your tires flat against them, to keep the tread in contact with the root's surface. Lean your bike at as close to the angle at which the obstacle slopes as you can, while keeping your body upright. Otherwise, only the edge of the tire will be touching the obstacle, and you'll slide to the bottom.