This is a bit tricky to explain.
There are two possible issues here.
The more obvious one is if you are not using an outline version (type 1) of the T1 fonts (eg, CM-Super), and are instead getting the bitmap (type 3) "EC" version. You can tell if this is the case because after zooming in very far you will see that the glyphs are "jagged". Alternatively, you can check the name of the embedded font (eg, sfrm1000 for CM-Super). Since the full set of type 1 CM-Super fonts is many megabytes, many tex distributions do not install it by default. See this FAQ answer and this one. You may have to install CM-super (or alternatively use lmodern).
The second possible issue is that the CM-Super fonts are indeed not as well constructed as the bluesky computer modern. This is a more subtle effect, and may not show up depending on your OS and your PDF viewer. It almost certainly is invisible when you print the PDF. Lmodern is a little better in this regard, but still not as good as computer modern.