Can you use Jinja without Bootstrap in Flask?
Jinja is a rendering engine. It doesn't care what it's rendering, and that includes not caring that you decided to use Twitter Bootstrap to lay out your HTML page.
wtf.form_field is a macro from Flask-Bootstrap that handles rendering the label, input, errors, and other information with Bootstrap's CSS. There is no requirement that you use it. You can look at its source to see what you would need to do instead.
There is nothing wrong with using pre-made CSS like Bootstrap, or libraries like Flask-WTF and Flask-Bootstrap, to handle parts of the application you don't want to deal with.
I've been building my Flask app from a little code I found in a tutorial. My Flask app is using Bootstrap, WTForms and Jinja to render the HTML files. I would like to clean up since I don't think I need Bootstrap.

Can you use Jinja and WTForms without Bootstrap? I'm pretty sure you
can but I found a lot of examples that have code like {{
wtf.form_field(form.username) }} which is making me insecure.
What is the advantage of {{ wtf.form_field(form.field1) }} instead
of {{ form.name.label }} {{ form.name(size=20) }}?
Can you use Flask without Bootstrap? I don't want to include
all those files.