The IRS Data Book for 2006 reports that 83,350 organizations completed IRS Form 1023s in order to apply for recognition of their 501(c)(3) tax exempt status. Of these, 67,545 were either accepted or rejected with the remaining 15,000 withdrawn, incomplete, or treated in other special ways.
Table 24 of the Data Book shows that for those that were either accepted or rejected, less than 2% (1,283) were disapproved.
The remaining types of exempt organizations (501(c)(4)s, etc.) accounted for less than 8% of total applications.
The Data Book is available on the IRS website.
http://www.irs.gov/taxstats/article/0,,id=102174,00.html