It's widely accepted that Google will penalize you somewhat if you have too many affiliate links and banners on your blogs and sites. I doubt that the effect is very great, though. Many of the big dogs of blogging, who continue to receive monster search engine traffic, have a lot of ads on their blogs.
In any case there are advantages in doing this. Obviously, you'll eventually make some sales with this method. Also, in some cases, your unique affiliate link can start to appear in the search engines. If it's ranking for a reasonably popular search term, you can get a nice flood of signups and sales that goes for quite some time, until it eventually slides off the first page. This has occurred occasionally with a few of the programs I've been promoting. As far as I can tell it resulted from having those unique affiliate links on blogs with good page rank.