On certain models the upper windshield molding vibrates at a higher speed causing a noise. Back filling the molding with silicone sealer will eliminate the noise.Google+
Car Problem Reports
Honda Civic Upper windshield molding may vibrate/make noise at higher speeds
Honda Civic Problem
Visitor, 1998 Honda Civic, 150,000 mi
Initially it was happening only on hot days at highway speeds - especially if I was facing south while driving. Took me a while to figure out the problem as it wouldn't start until I hit 50 mph and it would disappear around 70 mph. The mph range and temperature range grew over time. I finally tried masking tape over the seal along the top of the window and it worked! I replaced that with some clear caulk from the local parts store made for car windows and haven't had the issue in the past 5-6 years.