It depends on what you want. Do you want onesided printed documents or doublesided documents? One sided documents have the same margins on the right and left side, double sided documents have margins builded like this: outer margin = 2 * inner margin, for example for a right side:
outer margin (right one, 4cm) = inner margin (left one, 2cm) * 2
The result is that you get a good looking book with 3 same margins: left (4cm) = inner (2cm+2cm=4cm) = right (4cm).
Document class scrartcl and scrreprt are one sided, scrbookis doublesided. If you want to change this you can add the document class option oneside or twoside.
Try this MWE and play with the comment signs:
%http://tex.stackexchange.com/questions/85884/koma-script-unequal-left-right-margin
\documentclass[%
oneside % prints one sided; twoside is standard for scrbook
% twoside % prints double sided documents
,fontsize=11pt % fontsize for standard font
]{scrbook} % scrartcl scrreprt scrbook
\usepackage{amsmath,amssymb,amsfonts,hyperref}
\usepackage{showframe} % shows typing area with frames; for test only!
\begin{document}
\large
%%% Header %%%
\title{My Title}
\author{John J. Johnson}
\date{December 2012}
\maketitle
\end{document}
The inner title of a book is always printed in the area used in the book, the envelope of the book can be build differently.
If you want to make an envelope for your work, use a separate file with one sided printing. With KOMA-Script you can use the environment titlepage to create your own title pages. In the manual you will find this ...
titlepageenvironment is available in the standard LaTeX classes as well, but it's pretty useless imho (What does the titlepage environment do and what are its benefits?). Instead of changing the margins manually, I'd recommend using thetypeareacomponent of KOMA-Script, which can be used with non-KOMA classes as well, see http://tex.stackexchange.com/a/61847/4012. – doncherry Dec 07 '12 at 04:49