Homestead is running, as I have gulp watch running also and I can make changes. I have checked all the connections and they match the ones in the documentation and I am able to add new users etc and they appear in the database.
I have a .envexample which is unchanged and I have a ,.env file which has all my connections etc.
The database.php Is also unchanged from its default.
.env.example doesn't do anything, it is an example. You should remove it and place all your actual settings and sensitive data that you don't want in version control inside the .env file. I think that could be where you are going wrong.