Running a standalone program is difficult for any sized company but especially a smaller one...
Not only do you have to content with awareness but affiliates have to believe in the integrity of your system. Few people will find you and even fewer will believe that you're a reliable source versus all of the other large brands in the space.
If you do chose to peruse the direct route you'll want to get heavily integrated into webmaster & affiliate communities. Some will let you announce a program, others you can just reply to questions about yours and of course you get a signature / blog footer / profile depending on the site type.
But really if you want to make a program a big part of your marketing I'd suggest looking into a network. There's several major players (CJ, Pepperjam, Linkshare, Google, etc) who all have the trust and reach already.