With a good setup, and new pads, materials, cables, etc etc., road bikes with skinny tires have a harder time slowing down because of...

*drumroll*

...skinnier tires.

There's really two places where braking friction happens -- at the brakes themselves, and where the tire meets the road. You can slow down harder if you have more rubber on the road.

Still, you should be able to brake fine on a road bike. Just pay enough attention to your surroundings, don't ride at 35 mph in tight quarters (unless you're in a bike race, of course, or keeping up with street traffic), and plan ahead to avoid accidents.