Instead of trying to make makecell and colortbl compatible, I'd suggest dropping the usage of makecell. You can achieve the same layout without it as shown in the following MWE:
\documentclass{article}
\usepackage[table]{xcolor}
\definecolor{TopRow}{rgb}{0.4,0.7,1}
\definecolor{NormalRow}{rgb}{0.8,0.9,1}
\begin{document}
\begin{tabular}{|l|l|l|}
\hline
\rowcolor{TopRow}
\textbf{Peptide Enrichtments} & \textbf{Hits} & \textbf{Found Genes} \\
\hline
\rowcolor{NormalRow}
Nothing & 3 & RAB5C \\
\rowcolor{NormalRow}
& & TNKS1BP1 \\
\rowcolor{NormalRow}
& & WDR43 \\
\hline
20X dilution& 1 & AHCY \\
\hline
\rowcolor{NormalRow}
TiO2 & 2 & TNKS1BP1\\
\rowcolor{NormalRow}
& & ITPR2 \\
\hline
TiO2-3 &0& -\\
\hline
\rowcolor{NormalRow}
Fe-NTA & 0&- \\
\hline
\end{tabular}
\end{document}

As you use color as a structuring element in your table, you might also consider dropping all the horizonal and vertical rules. In the following example, I have also added a bit of extra vertical space:
\documentclass{article}
\usepackage[table]{xcolor}
\definecolor{TopRow}{rgb}{0.4,0.7,1}
\definecolor{NormalRow}{rgb}{0.8,0.9,1}
\begin{document}
\begingroup
\renewcommand{\arraystretch}{1.2}
\begin{tabular}{lll}
\rowcolor{TopRow}
\textbf{Peptide Enrichtments} & \textbf{Hits} & \textbf{Found Genes} \\
\rowcolor{NormalRow}
Nothing & 3 & RAB5C \\
\rowcolor{NormalRow}
& & TNKS1BP1 \\
\rowcolor{NormalRow}
& & WDR43 \\
20X dilution& 1 & AHCY \\
\rowcolor{NormalRow}
TiO2 & 2 & TNKS1BP1\\
\rowcolor{NormalRow}
& & ITPR2 \\
TiO2-3 &0& -\\
\rowcolor{NormalRow}
Fe-NTA & 0&- \\
\end{tabular}
\endgroup
\end{document}

This last example shows a more minimalistic approach without colors and bold text, but with white space and rules from the booktabs packages as structural elements:
\documentclass{article}
\usepackage{booktabs}
\begin{document}
\begin{tabular}{lll}
\toprule
Peptide Enrichtments & Hits & Found Genes \\
\midrule
Nothing & 3 & RAB5C \\
& & TNKS1BP1 \\
& & WDR43 \\\addlinespace
20X dilution & 1 & AHCY \\\addlinespace
TiO2 & 2 & TNKS1BP1 \\
& & ITPR2 \\\addlinespace
TiO2-3 & 0 & - \\\addlinespace
Fe-NTA & 0 & - \\
\bottomrule
\end{tabular}
\end{document}

colorboxaround themakecellcommands should yield the desired result. – leandriis Jun 11 '18 at 13:22makecellcompletely, as the layout in the table can also be achieved by using three separate rows for the first light blue row. This way you can continue usingrowcolor. – leandriis Jun 11 '18 at 13:58