Is rake db:migrate the correct command to re-sync schema.rb with your database schema?

"rake db:migrate" will try and run all the outstanding migrations for your project. If you just want to dump the schema do a "rake db:schema:dump".
But I think you have a problem where it says that the table already exists. One of your migrations is failing because the table it is trying to add already exists in your db. Did you create one by hand? Did you down a migration, but not have a down written for it? You will need to fix this before you can write future migrations. If it is just a mistake, and the table is there and correct and you want to ignore this. My recommendation is to hack around it by commenting out the create table in the failing migration. Then run "rake db:migrate". Then but the create table back. This will update your schema version.
Make sure you write proper downs on all migrations.

Try

RAILS_ENV=development rake db:drop

before

RAILS_ENV=development rake db:migrate

and be happy!

Making sure that you run it on your test or development environment since this will drop the database/tables

I've found that occasionally, when things get a little weird, you'll find yourself in a situation where Rails will want to run a migration that it ought rightly to be considering already done (the table already exists, etc). You can mark a migration as done by finding its number (the number part at the beginning of the filename), going into mysql and issuing a query like so:

insert into schema_migrations values('20090521153438');

(or whatever the number of your migration is)

Or if it's a plugin migration being run using Desert's migrate_plugin:

insert into plugin_schema_migrations values('my_plugin', '005');