For drupal 8, take a look into composer.json and checkout for 'extra' section. Add the file_mapping:
"drupal-scaffold": {
"locations": {
"web-root": "web/"
},
"file-mapping": {
"[web-root]/.htaccess": false
}
},
I found the solution in the README file for drupal-composer-scaffold: /vendor/drupal/core-composer-scaffold/README.md
There it is to be found when you installed drupal with the composer project drupal/recommended-project
Important
Do not miss security updates in .htaccess file: watch the diff in core/assets/scaffold/files/htaccess