Yes it is. Guinea pigs regulate the body temperature with the blood flow through the ears, so the ears need to be clear and not swathed in fur. Only worry if the patches are not symmetrical or suddenly get larger and sore.
Here is more about body quirks: http://www.theguineapigforum.co.uk/showthread.php?t=58854
We have other informative threads for newbies in our reference section, too, which you may find helpful.