How to improve the size of cells in this table?

Another redesign:

\documentclass[11pt,letterpaper]{article}
\usepackage{geometry}
\geometry{letterpaper, left=0.6 in, right = 0.6 in, top = 0.8 in, bottom= 0.8 in}
\usepackage{tabulary,booktabs}
\begin{document}
\begin{table}[h]
\centering\tabcolsep.6em 
\begin{tabulary}{\linewidth}{LCp{15em}p{8em}C}\toprule
 &  \multicolumn{3}{c}{Habilidades cognitivas} &  \\\cmidrule{2-4}
Ejes\par temáticos & ~\par Comprensión & ~\par Aplicación & Análisis, síntesis\newline y evaluación & ~\par Totales \\\midrule
 Números & 2 & 1--3--5--6--7--9--10--11--12--13--14--15 & 4--8--16--17 & 17 \\\addlinespace
 Álgebra & --- & 18--19--20--21--22--23--24--26--28--29--30--31--32--33--34--35 & 25--27--36 & 19 \\\addlinespace
 Geometría & --- & 37--38--39--40--41--42--43--44--45--46--48--49--50--51--52--53--54--55--56--57 & 47--58 & 22 \\\addlinespace
 Datos y azar & 60--64 & 59--61--62--63--65--66--67--68--70--71--72--73--74--75--76--77--78--79 & 69--80 & 22 \\\bottomrule
\end{tabulary}
\end{table}
\end{document}

Maybe you can also use a more compact version with a comma separated list and ranges:

\documentclass[11pt,letterpaper]{article}
\usepackage{geometry}
\geometry{letterpaper, left=0.6 in, right = 0.6 in, top = 0.8 in, bottom= 0.8 in}
\usepackage{booktabs}
\begin{document}
\begin{table}[h]
\centering\tabcolsep.6em 
\begin{tabular}{lcccc}\toprule
 &  \multicolumn{3}{c}{Habilidades cognitivas} &  \\\cmidrule{2-4}
Ejes\par temáticos & ~\par Comprensión & ~\par Aplicación & Análisis, síntesis\newline y evaluación & ~\par Totales \\\midrule
 Números & 2 & 1, 3, 5--7, 9--15 & 4, 8, 16--17 & 17 \\
 Álgebra & --- & 18--24, 26, 28--35 & 25, 27, 36 & 19 \\
 Geometría & --- & 37--46, 48--57 & 47, 58 & 22 \\
 Datos y azar & 60, 64 & 59, 61--68, 70--79 & 69, 80 & 22 \\\bottomrule
\end{tabular}
\end{table}
\end{document}

See, if you liked the following "redesign" of your table:

\documentclass[11pt,letterpaper]{article}
\usepackage[letterpaper]{geometry}
\usepackage[spanish]{babel}
\usepackage{makecell, multirow, tabularx}
\renewcommand\theadfont{\small\bfseries}
\renewcommand\theadgape{}

\begin{document}
\begin{table}[ht!]
    \setcellgapes{3pt}
    \makegapedcells
%    \small
\begin{tabularx}{\linewidth}{|>{\bfseries}l|p{4.4em}|>{\hsize=1.2\hsize}X|>{\hsize=0.8\hsize}X|c|}
    \hline
\multirow{3}{*}{\thead{Ejes\\ Temáticos}} 
    & \multicolumn{3}{c|}{\thead{Habilidades Cognitivas}} 
            & \multirow{3}{*}{\thead{Totales}}                     \\
    \cline{2-4}    
    &  \thead{Com-\\prensión} 
        & \thead{Aplicación} 
            & \thead{Análisis, Síntesis\\ y Evaluación} 
                                &       \\
    \hline
Números 
    & 2 & 1 - 3 - 5 - 6 - 7 - 9 - 10 - 11 - 12 - 13 - 14 - 15 
            & 4 - 8 - 16 - 17   & 17    \\
    \hline
Álgebra 
    &   & 18 - 19 - 20 - 21 - 22 - 23 - 24 - 26 - 28 - 29 - 30 - 31 - 32 - 33 - 34 - 35 
            & 25 - 27 - 36      & 19    \\
    \hline
Geometría
    &   & 37 - 38 - 39 - 40 - 41 - 42 - 43 - 44 - 45 - 46 - 48 - 49 - 50 - 51 - 52 - 53 - 54 - 55 - 56 -  57      & 47 - 58           & 22    \\
    \hline
\thead[lt]{Datos\\ y Azar}
    & 60 - 64
        & 59 - 61 - 62 - 63 - 65 - 66 - 67 - 68 - 70 - 71 - 72 - 73 - 74 - 75 - 76 - 77 - 78 - 79
            & 69 - 80           & 22    \\
    \hline
\end{tabularx}
    \end{table}
\end{document}

Edit:

For beter positioning of contents in the last row I add option t to \thead: \thead[lt]{Datos\\ y Azar}