According an the article (DOI:10/.1126/science.1066355) there are 2000 to 3000 transcription factors. How many of them have a known TFBS (transcription factor binding sites) in humans. This answer could be derived bioinformatically or by a citation.
If I look at the TRANSFAC release dated Mar 2010, there are 1300 TFBS matrices given. This includes minor variations like V$P53_03 V$P53_04 V$P53_05 and so on. If I restrict my search to vertebrates the number is 908. If I ignore the part after the '_', the number works out to 598. While this is vertebrates and not just humans you could get some idea of the numbers involved.
I have 245 human transcription factors with motifs described in TRANSFAC and/or JASPAR.
I also use data published by Xie, et al (Xie, Z., Hu, S.H., Blackshaw, S., Zhu, H. and Qian, J. (2009) hPDI: a database of experimental human protein-DNA interactions, Bioinformatics. (In press); http://bioinfo.wilmer.jhu.edu/PDI/) which gives sequence motifs for known and non-traditional DNA-protein interactions. From those data, I extracted 1015 genes.
The data is spread over at least three databases: Transfac, Jaspar and UniProbe. You could drop Transfac, it's a rather strange datasource. You would need to parse the (human) gene identifiers from Jaspar and Uniprobe and then get the union of them.