Yeah, water always gets in if you change a tire in the rain, but a tubular always seems to get me home OK. The system is reasonably forgiving. The hard part is on a freezing, rainy day, when your hands are blocks of ice, and you have to pry that danged flatted tire off the rim.
Tufo sells a really nice tubular tire bag (Roger has them at
www.worldclasscycles.com), which is better than the traditional alternative of an old sock. I always put the tire inside a big ziploc bag inside the tire bag, both so a rainy ride doesn't get any water on it and because the plastic helps minimize any chafing of the tire.