You are correct. The 13.9% “taxes” Romney paid IS NOT his entire tax contribution-—it just looks good for “headlines!” Romney paid A LOT higher rate on his taxes, each year. (The news media ALWAYS “forgets” to count the tax rate the rich pay on capital gains!!! Which is what, another 30-35%? Then ADD THAT to the 13.9% and you have a tax rate not too far off from 50%.
What's your source for this claim? "Romney pays a 14-15% tax rate, lower than many taxpayers." - http://www.forbes.com/sites/kellyphillipserb/2012/01/24/romneys-tax-returns-are-remarkably-unremarkable/