analysis of RC circuit using Matlab
You have two sets of waveforms 

1) time domain

2) frequency domain 

While you will see a difference between the two time domain plots (higher frequency resulting in a lower output, as expected) you will not between the two frequency domain plots

Why?  it is how the matlab command works. You are not instructing Matlab to provide gain:phase at a particular frequency for the two frequency domain plots, you have essentially instructed Matlab to run a frequency sweep and resultant bode plot twice.

As a result you will not see any difference between these two plots.

--edit--
Based upon the presented matlab code:

The simplest solution to demonstrate a difference at different frequencies is to change the bode function call from

bode(monSysteme) 

to 

bode(monSysteme,{249,251})

and also:

bode(monSysteme,{1999,2001})

ie a specific frequency range, tight to the freq of interest.




PLEASE note, this isn't really needed as you can just read off of the original bode plot the magnitude at 250Hz and 2kHz and see a difference.

If a specific time domain reference point is needed &amp; the desire isn't to read the result off of a bode plot then the BODE command isn't the correct command but lsim with a specific stim:

R=1e3;
C=0.15e-6;
num=1;
denum = [R*C 1];
m = tf(num,denum);

[u,t] = gensig('sin',1/250);
lsim(m,u,t)
figure
[u,t] = gensig('sin',1/2000);
lsim(m,u,t)