If you want the logo to appear centered in the footline, you need to redefine the footline template as implemented by the frame number option (original code in beamerbaseauxtemplates.sty) and to set the sidebar right template to be empty (this is the template where the logo goes in the default theme). The following example shows this redefinition (you might need to adjust the lengths in the \raisebox to suit your needs):
\documentclass[t]{beamer}
\beamertemplatenavigationsymbolsempty
\setbeamertemplate{footline}[frame number]
\logo{\includegraphics[width=.5cm,keepaspectratio]{tux}}
\setbeamertemplate{sidebar right}{}
\defbeamertemplate*{footline}{logo-frame number}
{
\rlap{\raisebox{-1.75ex}[0pt][0pt]{\makebox[\paperwidth]{\insertlogo}}}%
\hfill%
\usebeamercolor[fg]{page number in head/foot}%
\usebeamerfont{page number in head/foot}%
\insertframenumber\,/\, \inserttotalframenumber\kern1em\vskip2pt%
}
\begin{document}
\begin{frame}[c]{Hello world}
\begin{itemize}
\item item 1
\item item 2
\item item 3
\end{itemize}
\end{frame}
\end{document}
The result:

If all you want to do is to flush the logo to the left, all you have to do is to get ride of your \makebox:
\documentclass[t]{beamer}
\beamertemplatenavigationsymbolsempty
\setbeamertemplate{footline}[frame number]
\logo{\includegraphics[width=.5cm,keepaspectratio]{tux}}
\begin{document}
\begin{frame}[c]{Hello world}
\begin{itemize}
\item item 1
\item item 2
\item item 3
\end{itemize}
\end{frame}
\end{document}
The result:
