This is an interesting question that has come up many times over the past few years. It is an issue that many confuse with being a Google Analytics issue...it's not, it is a Google issue affecting ALL web analytics tools. Essentially what is happening is a proportion of Organic traffic is being dumped into 'Direct' incorrectly, and is caused primarily by browsers failing to correctly report where traffic is coming from, with IE being the biggest culprit.
There are many potential issues as to why browsers aren't helping analytics packages like Google Analytics report traffic sources correctly and they include the issue that browsers cannot report when a visit transits from HTTPS to HTTP. Also, tracking the referrer is difficult depending on the search box used, browser security setting and even Apple's IOS caused issues back in September 2012 when organic referrer data was 'lost' overnight but brands noticed a remarkable and equal uplift in Direct visits.
So Organic data records will never be 100% accurate...
So we know it happens so how can we account for it?
A great example of this was a very crude test performed by Groupon. Here they decided to understand what the 'true' Organic visitor 'loss' to Direct was by de-indexing themselves from Google for 6 hours and monitored the results. Long story short, within the 6 hours of down-time, their Organic traffic dropped to zero, while their Direct traffic dropped 60%!!! This fairly dramatic trial proved that for Groupon, they were under reporting their Organic visibility by up to 60%!
We are not advising this type of aggressive trial should be undertaken by any of our clients, as the damage from a search engine rankings point of view could be massive, but certainly bear this study in mind when looking at your website data.