The following code:
\documentclass[journal,twocolumn,10pt]{IEEEtran}
\usepackage[compress]{cite}
\usepackage{times} % Font Times New Roman throughout the document
\usepackage{subfigure}
\usepackage{epsfig}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{array}
\usepackage{algorithm}
\usepackage{algorithmic}
\usepackage{tikz,pgfplots}
\usepackage{adjustbox}
\pgfplotsset{compat=1.14}
\usepgfplotslibrary{patchplots}
\usepgfplotslibrary{fillbetween}
\usepackage{caption}
\usetikzlibrary{arrows.meta}
\usepackage{graphicx}
\usepackage{float}
\usepackage{mathtools}
\begin{document}
\begin{figure}[t]
\centering
\captionsetup{justification=centering}
\resizebox {0.8 \columnwidth}{!}{
\subfigure[Line]{\centering
\begin{tikzpicture}
\draw (0,0) node {$S= \begin{bmatrix}
0 & 0 & 0 & 0\\
1 & 0 & 0 & 0\\
0 & 1 & 0 & 0\\
0 & 0 & 1 & 0\\
1 & 0 & 1 & 0\\
0 & 0 & 0 & 1\\
1 & 0 & 0 & 1\\
0 & 1 & 0 & 1\\
\end{bmatrix}$};
\end{tikzpicture} }
\subfigure[Square]{\centering
\begin{tikzpicture}
\draw (0,0) node {$S= \begin{bmatrix}
0 & 0 & 0 & 0\\
1 & 0 & 0 & 0\\
0 & 1 & 0 & 0\\
0 & 0 & 1 & 0\\
1 & 0 & 1 & 0\\
0 & 0 & 0 & 1\\
0 & 1 & 0 & 1\\
\end{bmatrix}$};
\end{tikzpicture}}
}\\
\resizebox {0.8 \columnwidth}{!}{
\subfigure[Full]{\centering
\begin{tikzpicture}
\draw (0,0) node {$S= \begin{bmatrix}
0 & 0 & 0 & 0\\
1 & 0 & 0 & 0\\
0 & 1 & 0 & 0\\
0 & 0 & 1 & 0\\
0 & 0 & 0 & 1\\
\end{bmatrix}$};
\end{tikzpicture}}
\subfigure[Star]{\centering
\begin{tikzpicture}
\draw (0,0) node { $S= \begin{bmatrix}
0 & 0 & 0 & 0\\
1 & 0 & 0 & 0\\
0 & 1 & 0 & 0\\
0 & 0 & 1 & 0\\
0 & 1 & 1 & 0\\
0 & 0 & 0 & 1\\
0 & 1 & 0 & 1\\
0 & 0 & 1 & 1\\
0 & 1 & 1 & 1\\
\end{bmatrix}$};
\end{tikzpicture}}}
\caption{Action rule matrices for network graphs of figure \ref{NETEXAMPLE}}
\label{ACTIVATIONFIG}
\end{figure}
\end{document}
produces the following picture:

which horizontally align the matrices setting the captions in the same row to be aligned. I would like to align matrices of the same row to have the S= at the same height (aligned S's in two rows).
Regards




subcaption, you should removesubfigure(which is obsolete). – Zarko Jun 20 '18 at 16:20