Use Checkboxes with Drupal Better Exposed filter
This also tripped me up. The settings weren't where I expected them to be and there were a couple of prerequisites. Maybe this is your issue too?


Create a View and expose a filter
Under Advanced > Exposed form > Exposed form style select Better Exposed Filters
Under BEF Settings roll down to the bottom where there are the Exposed Filter settings and select Checkboxes/Radio Buttons from the drop down menu.


Note: You can't select these settings for filters that don't have a limited number of options. (A title won't work, but a term will.) The documentation says:


  BEF only operates on fields that have a limited number of options such as Node:Type or Taxonomy:TermID. Open-ended fields, such as Node:Title, do not work with BEF. Entity References do work, however, if you Enable Render Views filters as select list (a checkbox) in the Entity's entityreference field.


I had utilized the entity reference field pattern. You need to edit the field you are referencing in the Content types > [content type] > manage fields > [field name] > edit. field settings. There, at the bottom of the page under Additional Behaviours you will find a checkbox for Render Views filters. That will allow the aforementioned select box (in BEF settings) to properly display the Checkbox/Radio option.