Assuming that every entry in your table also uses \ch, you can define your own command as follows:
\documentclass[11pt,a4paper]{report}\usepackage[utf8]{inputenc}\usepackage[left=1.00cm, right=1.00cm, top=1.00cm, bottom=1.00cm]{geometry}\usepackage{colortbl}\usepackage{chemformula}\newcommand{\redch}[1]{\textcolor{red}{\ch{#1}}}\begin{document} \begin{center} \footnotesize \renewcommand{\arraystretch}{1.5} \hspace*{-1cm}\begin{tabular}{|c|c|c||c|c|c|c|c|c|c|c|} \hline \rowcolor{black} \multicolumn{11}{|c|}{\textcolor{white}{Corps purs}}\\\hline \rowcolor{gray!90}élémentaires& \multicolumn{2}{c||}{simples} & \multicolumn{8}{c|}{composés}\\ \hline \rowcolor{gray!70}&métal.& non-métal. & \multicolumn{2}{c|}{Oxydes} & Hydroxydes & \multicolumn{2}{c|}{Acides} & \multicolumn{2}{c|}{Sels} & Corps organiques\\ \hline \rowcolor{gray!50}&& & métal. & non-métal. & & bin. & tern. & bin. & tern. &\\ \hline && & & & & & & & &\redch{C6H12O6}\\ \hline && \redch{Fe2O3} & & & & & & & &\\ \hline && & & & & & & & &\\ \hline&& & & & & & & & &\\ \hline&& & & & & & & & &\\ \hline&& & & & & & & & &\\ \hline \end{tabular} \end{center}\end{document}You could also use \setchemformula{format=\color{red}} inside of the center environment to change the color of a \ch inside of that environment:
\documentclass[11pt,a4paper]{report}\usepackage[utf8]{inputenc}\usepackage[left=1.00cm, right=1.00cm, top=1.00cm, bottom=1.00cm]{geometry}\usepackage{colortbl}\usepackage{chemformula}\begin{document} \begin{center} \setchemformula{format=\color{red}} \footnotesize \renewcommand{\arraystretch}{1.5} \hspace*{-1cm}\begin{tabular}{|c|c|c||c|c|c|c|c|c|c|c|} \hline \rowcolor{black} \multicolumn{11}{|c|}{\textcolor{white}{Corps purs}}\\\hline \rowcolor{gray!90}élémentaires& \multicolumn{2}{c||}{simples} & \multicolumn{8}{c|}{composés}\\ \hline \rowcolor{gray!70}&métal.& non-métal. & \multicolumn{2}{c|}{Oxydes} & Hydroxydes & \multicolumn{2}{c|}{Acides} & \multicolumn{2}{c|}{Sels} & Corps organiques\\ \hline \rowcolor{gray!50}&& & métal. & non-métal. & & bin. & tern. & bin. & tern. &\\ \hline && & & & & & & & &\ch{C6H12O6}\\ \hline && \ch{Fe2O3} & & & & & & & &\\ \hline && & & & & & & & &\\ \hline&& & & & & & & & &\\ \hline&& & & & & & & & &\\ \hline&& & & & & & & & &\\ \hline \end{tabular} \end{center}\end{document}