It's not a matter of good or bad. I would say its a question of deployment or even business context.
Do you need to Drop all the tables (hence the data) and recreate them? If it's a fresh deployment, then it doesn't really make a difference. If you already have the production database, I do not see why you would want to drop the existing tables unless in scenarios like an overhaul or total revamp.
UPDATE:
For you case, it's a good start to have the DB created according to the Hibernate mapping, saves you some time. I would not recommend it for direct production use without it being tested say for development or staging. I use NHibernate's tools to generate the schema for my DB as well, but it is for me to verify that my mapping works and I tweaked it along the way. The final production-ready schema is actually a copy from my staging DB. But it should work well for you to use your method.
In short, always double check.