\documentclass[twocolumn]{jsarticle}
% \footnoterule の定義を保存
\let\origfootnoterule\footnoterule
\usepackage{ftnright}
\global\let\footnoterule\origfootnoterule
\usepackage{ifthen}
\newcounter{hoge}
\newcommand\hoge[1][1000]{\whiledo{\value{hoge}<#1}{%
  \stepcounter{hoge}ほげ}\footnote{脚注なり。}。\setcounter{hoge}{0}}
\gdef\footnoterule{\kern-3pt \hrule width .4\columnwidth \kern 2.6pt}
\begin{document}
\author{An Author}
\title{A Title}
\maketitle
\section{はじめの節}
\hoge[50] \hoge[50] \hoge[70] \hoge[100]
\section{次の節}
\hoge \hoge[20] \hoge[30] \hoge[50]
\end{document}
