gulp minify all css files to a single file

Your gulp task is missing the concat pipe.

gulp.src('src/css/**/*.css')
    .pipe(minifyCSS())
    .pipe(autoprefixer('last 2 version', 'safari 5', 'ie 8', 'ie 9'))
    .pipe(concat('style.min.css'))
    .pipe(gulp.dest('dist/css'))

Here is a very good tutorial about building with gulp:

http://www.smashingmagazine.com/2014/06/11/building-with-gulp/