The publisher is able to override the reader's choice of font family and many other settings from the book if they choose to do so. Converting a book to epub with Calibre can also have a similar unfortunate effect due to the CSS 'flattening' that Caibre does.
There are some
firmware patches that can help with some settings such as line spacing, but they are not a perfect solution. The only real solution is to edit the book's stylesheet before sideloading the book and remove the publisher's overriding styles.
Edit: To better answer the question: There isn't usually one specific setting that you can change in the stylesheet to fix the problem, but for font-family a general procedure that often works is to remove the font-family property from div/p/span elements that are used for the main body of text and add it to the body element instead, and let the div/p/span inherit the property from body. Leave in place the font-family properties for special elements such as headings etc. That way you can see the publisher's original setting by selecting the "Document Default" font, and special elements such as headings will remain in the publisher's font, but selecting a different font from the device will change the main body of text.
Edit2: A blunter approach for font-family is simply to strip all font-family styles and all embedded fonts from the book. However that can spoil some books which depend on different font styles as an integral part of the story, e.g. to indicate different speakers; and detract from other books which simply make some nice use of fonts in appropriate places, such as fancy headings or a handwriting font for extracts from a diary.