I am trying to redirect all user requests to a bootstrap file, but when I do that the CSS and other files redirected.
How I can prevent this?
You can preface your rewrite rule with the following two lines to check if a file/directory exists before rewriting:
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ...
If you want to whitelist only certain files/folders, you can exclude them in the rule itself:
RewriteRule ^(?!css|js|images|testfile\.php) ...