The appearance of the image is also affected by the jobotpions file (as mentioned earlier) usd to create the PDF. There are settings that will automatically downsample high-res images and will apply additional jpg (lossy) compressions to pre-existing jpgs - all of which downgrade an image. You need to set these options accordingly.
Also, having a very high-res image increases the load time for the page, which often tends to annoy readers. Something else that you should consider, especially if it is on every page.
If you want to preserve maximum fidelity of a logo at any zoom level, then using vector-based artwork (also already mentioned) should have been the primary consideration (but this will also increase load time as the vectors need to be drawn).