Is it due to my eyes that these words W1 aren't of the same size here? Also I tried left aligned for the second column but somehow it looks skew to me. Please tell me if you have any idea to make it look nicer.
\documentclass[journal]{IEEEtran}
\usepackage{amsmath,amsfonts}
\usepackage[caption=false,font=normalsize,labelfont=sf,textfont=sf]{subfig}
\usepackage{booktabs}
\begin{document}
\begin{table}[!h]
\centering
\caption{TEST FUNCTIONS}
\label{tab:table1}
\begin{tabular}{c l}
\toprule
STTC & FUL\\ \midrule
H1 & $W_1$ \\\midrule
H2 & $\frac{1}{W_1}$ \\\midrule
H3 & $\frac{1}{1-W_1}$ \\\midrule
H4 & $1-W_1$ \\\midrule
H5 & $\frac{W_1-1}{W_1}$ \\\midrule
H6 & $\frac{W_1}{W_1-1}$\\\bottomrule
\end{tabular}
\end{table}
\end{document}
$... $
is always text style math (unless under certain circumstances)\dfrac
instead of\frac
to get display fractions.