Notice that in each iteration of your loop you plot one point: (A(i),B(i)). That's why only the end of the pendulum shows up. If you want to show the entire pendulum moving, you have to plot two points - the other one being the fixed point at the top of the pendulum, (0,L), which is also (A(1),B(1)).
L = 2;
g = 9.81;
squarerootvalue_gl = sqrt(g./L);
squarerootvalue_lg = sqrt(L./g);
T = 2 .* pi .* squarerootvalue_lg;
t = 0:0.01:T;
theta = pi./3 .* cos(squarerootvalue_gl*t);
x = L .* sin(theta);
y = L .* (1 - cos(theta));
A = [0 x];
B = [L y];
figure
temp = [min(A) max(A)];
axis([temp 1+temp]);
p = line(NaN, NaN, 'Color','b', 'Marker','.', 'MarkerSize', 10);
for i = 2:length(t)
set(p,'XData',A([1 i]),'YData',B([1 i]));
drawnow
end
