WordPress theme options allow you to change things like fonts, colours, logos and many other design elements across your website, from header to footer. Custom Theme Options mean you can truly customise your website. This is particularly useful for many reasons, including; certain times of the year when you need to change your colouring, or if you go under a brand revision and updates to your fonts or logo need to be made without a full site rebuild.
Be careful! Changing things can be hazardous, so before you make any changes please consult your site specific documentation.