did you look at the website in the Web Tools of your browser? most likely the console will show that your css is 404. That is because when you have the site as a GH project, the actual site path is as a sub folder of your username. So the path to the css needs to include the project name - it is not /assets/css.
This is what baseurl is for - in the config you can set a value for baseurl that is your project name followed by a slash. Then you can prepend baseurl or siteurl(?) to all your static files to get the correct path.