Looking at the definition of the beamer templates mini frame/mini frame in current subsection in beamerouterthemedefault.sty (ll. 21-39), you'll see that the mini frames have a fixed size of 1mm. To change this according to your needs, these templates have to be redefined. This can be done using the following code:
\makeatletter
\newdimen\beamer@miniframeradius
\beamer@miniframeradius=0.05cm
\define@key{beamer@margin}{mini frame radius}{\beamer@miniframeradius=#1\relax}
\setbeamertemplate{mini frame}
{%
\begin{pgfpicture}{0pt}{0pt}{2\beamer@miniframeradius}{2\beamer@miniframeradius}
\pgfpathcircle{\pgfpoint{\beamer@miniframeradius}{\beamer@miniframeradius}}{\beamer@miniframeradius}
\pgfusepath{fill,stroke}
\end{pgfpicture}%
}
\setbeamertemplate{mini frame in current subsection}
{%
\begin{pgfpicture}{0pt}{0pt}{2\beamer@miniframeradius}{2\beamer@miniframeradius}
\pgfpathcircle{\pgfpoint{\beamer@miniframeradius}{\beamer@miniframeradius}}{\beamer@miniframeradius}
\pgfusepath{stroke}
\end{pgfpicture}%
}
\makeatother
Input this code in the preamble of your document, i. e. between \documentclass{beamer} and \begin{document}. It defines a new beamer length called mini frame radius which controls the size of the mini frames. The space that two mini frames are apart is set with mini frame size (which is not a very suitable name, but it's introduced by beamer like this). So to enlarge the mini frames, use \setbeamersize to change these length, e. g. like this:
\setbeamersize{mini frame radius=.07cm,mini frame size=.18cm}
Minimal test code:
\documentclass{beamer}
\useoutertheme{miniframes}
\makeatletter
\newdimen\beamer@miniframeradius
\beamer@miniframeradius=0.05cm
\define@key{beamer@margin}{mini frame radius}{\beamer@miniframeradius=#1\relax}
\setbeamertemplate{mini frame}
{%
\begin{pgfpicture}{0pt}{0pt}{2\beamer@miniframeradius}{2\beamer@miniframeradius}
\pgfpathcircle{\pgfpoint{\beamer@miniframeradius}{\beamer@miniframeradius}}{\beamer@miniframeradius}
\pgfusepath{fill,stroke}
\end{pgfpicture}%
}
\setbeamertemplate{mini frame in current subsection}
{%
\begin{pgfpicture}{0pt}{0pt}{2\beamer@miniframeradius}{2\beamer@miniframeradius}
\pgfpathcircle{\pgfpoint{\beamer@miniframeradius}{\beamer@miniframeradius}}{\beamer@miniframeradius}
\pgfusepath{stroke}
\end{pgfpicture}%
}
\makeatother
\setbeamerfont{headline}{size=\fontsize{9}{11}}
\setbeamersize{mini frame radius=.08cm,mini frame size=.2cm}
\begin{document}
\section{section 1}\subsection{subsection 1}
\frame{}\frame{}\frame{}
\subsection{subsection 2}
\frame{}\frame{}
\end{document}
Result:
