If you set the pos option to H (from the float package) then you can enclose your ctables inside minipages:
\documentclass{article}
\usepackage{booktabs}
\usepackage{ctable}
\usepackage{float}
\begin{document}
\begin{center}
\begin{minipage}{.5\textwidth}
\ctable[caption = Two ctables side by side,
label = tab:test1,
width = 5cm,pos= H,left]{c>{\raggedright}X}{
\tnote{footnotes are placed under the table}
}{
\ML
\multicolumn{2}{c}{Multicolumn entry!}
\NN
\midrule
one&
The width of this column depends on the width of the table.\tmark
}
\end{minipage}%THIS COMMENT IS SIGNIFICANT
\begin{minipage}{.5\textwidth}
\ctable[caption = Two ctables side by side,
label = tab:test2,
width = 5cm,pos= H,left]{c>{\raggedright}X}{
\tnote{footnotes are placed under the table}
}{
\ML
\multicolumn{2}{c}{Multicolumn entry!}
\NN
\midrule
one&
The width of this column depends on the width of the table.\tmark
}
\end{minipage}
\end{center}
\end{document}

Of course, now your tables are not floating objects so their correct placement is your responsibility.