Google has started protecting signed in users by not reporting their search terms, instead we see a (not provided). People have written this off saying that the number is insignificant, in fact you can make use of this nifty little Custom Report to check the impact of how many searches are not reported to you. Over a period of time, it has grown to be a huge 39% of the total organic results worldwide.
Blog owners have every right to be concerned; they are missing data and for content driven blogs, this can be painful. I have noticed that for all my games posts, the %age is quite high … 70%!!!
However, there is an alternative. If you are concerned with finding out the keyword data about your site, then you can retrieve this data from Google Webmasters (GWMT). This in combination with the Top Content Report for the Non-Paid search traffic segment should get you any data you require.
Combining the GWMT data with Analytics will help you get a better understanding for the funnel data on each of your individual keywords … all the more so if you have Goals configured.
Do note that there is a slight discrepancy in the data that is reported in GA and the one which is reported in WMT. GA reports visits, WMT reports clicks. GA’s SEO report does not provide the data of the past 2 days, WMT does. So if you are just starting out, using WMT would help you gain more insights on your on-page optimization as compared to simply using Google Analytics.
Edit: I found this great (but a tad tedious) article on SEOMoz on how you can decode the (not provided) keyword. If you are not well versed with Google Analytics and Filters, then I would suggest you skip it.