Your example won't work, take a look what you have :
<link rel="stylesheet" href="customTheme.min.css" />
<link rel="stylesheet" href="http://code.jquery.com/mobile/1.3.1/jquery.mobile.structure-1.3.1.min.css" />
<link rel="stylesheet" href="http://code.jquery.com/mobile/1.3.1/jquery.mobile-1.3.1.min.css" />
There are 3 different css files. First one is your custom theme, second one is only structure css file (everything else), and last one is complete jQuery Mobile css file. Currently your last css file (complete one) is overriding custom css theme.
To solve your problem change everything to:
<link rel="stylesheet" href="http://code.jquery.com/mobile/1.3.1/jquery.mobile-1.3.1.min.css" />
<link rel="stylesheet" href="customTheme.min.css" />
<link rel="stylesheet" href="http://code.jquery.com/mobile/1.3.1/jquery.mobile.structure-1.3.1.min.css" />
Or even better remove jquery.mobile-1.3.1.min.css
and use only:
<link rel="stylesheet" href="customTheme.min.css" />
<link rel="stylesheet" href="http://code.jquery.com/mobile/1.3.1/jquery.mobile.structure-1.3.1.min.css" />
What you need to understand, jQuery Mobile have 3 available css files. jquery.mobile-1.3.1.min.css
should be used alone because it hase css for themes and structure. If you have custom themes then you only need to use custom theme css file and jquery.mobile.structure-1.3.1.min.css
.
EDIT :
Don't forget that you also need to add data-theme
to your page DIV container:
<div data-role="page" id="home" data-theme="b">
or you can add it only to your header, content and footer DIV's but I would advise you to add it to page DIV.