You introduced some spurious space by adding new lines in your code. Just get rid of the new lines or use %
at its end. The very problem here was your seventh line of code.
% arara: pdflatex
\documentclass{beamer}
\usepackage{booktabs}
\begin{document}
\begin{frame}
\begin{tabular}{ll}
\toprule
Foo & Bar\\
\midrule
\alt<2>{\textbf{Foo} & \textbf{Bar}
}{% % you had an extra space here introduced by the new line of code. Write it on one line or add an % at the end of it.
Foo & Bar}\\
Foo & Bar\\
\bottomrule
\end{tabular}
\end{frame}
\end{document}
Apart from this, I would recommend to use \begin{tabular}{*{2}{p{.585cm}}}
. Like this, your 'animation' will result better...
% arara: pdflatex
\documentclass{beamer}
\usepackage{booktabs}
\begin{document}
\begin{frame}
\begin{tabular}{*{2}{p{.585cm}}}\toprule
Foo & Bar\\\midrule
\alt<2>{\textbf{Foo} & \textbf{Bar}}{Foo & Bar}\\
Foo & Bar\\\bottomrule
\end{tabular}
\begin{tabular}{*{2}{l}}\toprule
Foo & Bar\\\midrule
\alt<2>{\textbf{Foo} & \textbf{Bar}}{Foo & Bar}\\
Foo & Bar\\\bottomrule
\end{tabular}
\end{frame}
\end{document}
}{%
. You are inserting some spurious space in your seventh line of code. Please make your example compilable. This makes it easier for us to help. Thanks.