You can change the face color of the box:
square = rectangle('Position', [0, 0, 2.5, 15], 'EdgeColor','b','LineWidth',2,"FaceColor", "g");
You also need to change the order of box and text. MATLAB draw the object layer by layer. If you want to show text on top of box, you have to plot box first.
%% Header
% Written by C. Vogen
% Date Written:3/3/2024
% Modified: None
%% Variable Glossery
% t_start = 0; % seconds
% t_end = 10; % seconds
% x_final = 10; % meters
% y_final = 0; % meters
% g = 9.81 % m/s^2
% m = 150;
%
%% Code Statements
clear; clc; close all;
t_start = 0; % seconds
t_end = 10; % seconds
x_final = 10; % meters
y_final = 0; % meters
g = 9.81; % m/s^2
v_x0 = x_final/t_end; % finding initial x velocity
v_y0 = (y_final + (g*0.5*(t_end^2)))/t_end; % finding initial y velocity
m = 11;
T = zeros(m,2);
incrv = (t_end - t_start)/(m-1);
startCannon =[0,0]; endCannon = [.175,10]; % starts the cannon
Cannon = [startCannon;endCannon];
figure
plot(Cannon(:,1),Cannon(:,2),'LineWidth',5)
xlabel('x [m]');xlim([-1 13])
ylabel('y [m]');ylim([0 150])
hold on
pause(1)
Color_start = [.25 .25 .25];
Color_end = [1 1 0];
Color_incv = (Color_end - Color_start)/(m-1);
square = rectangle('Position', [0, 0, 2.5, 15], 'EdgeColor','b','LineWidth',2,"FaceColor", "g");
flag_text = text(0, 0, '', 'HorizontalAlignment', 'left','VerticalAlignment','bottom', 'FontWeight', 'bold');
for i = 1:m
t = t_start +(i-1)*incrv;
x = v_x0 * t;
y = (v_y0 * t) - ((g * t^2)/2);
Color = Color_start +(i-1)*Color_incv;
pause(0.4)
if i>1
delete(ball) % removing the previous marker
delete(line) % removes the line connecting the box to the point
end
ball = plot(x,y,'o','MarkerFaceColor','r'); % plotting inside the loop
set(ball, 'XData',x, 'YData',y)
set(flag_text, 'Position', [x+0.2, 30], 'String', {['X: ', num2str(x)], ['Y: ', num2str(y)],['I: ', num2str(i)],['T: ',num2str(t)]})
set(square, 'Position', [x, 25, 2.5, 38]);
line = plot([x,x],[0,30],'b','LineWidth',2);
axis normal
title('Visual Loop')
xlabel('x [m]');xlim([-1 13])
ylabel('y [m]');ylim([0 150])
grid on
end
