See my recent post at BlueObelisk StackExchange.
Wolf Ihlenfeldt's reply is very interesting for people that want to know more about PubChem fingerprints.
As he says, the SMARTS patterns (terminal part of the FPs)...
"are the result of capturing and analyzing user queries on the old NCI Cancer Screening database Web interface. They are intended to capture features which are used in actual queries. They were not designed specifically for similarities or correlation with any properties, but it turns out that there are indications that these screens work about as well as others in that sector".