Doing Putrajaya on your own is pretty much hopeless. I've toured it twice: once by chartering a taxi for an hour (RM 50-ish) and once by taking a public tour (RM 1 + tip). I'm usually very much a non-tour person, but the guide was quite good, the group was manageably small and at that price you can't complain! KL Transit (the rail company) also does "Explore Putrajaya" packages out of KL for around RM 20 including return train ticket and guided tour.
And a few links so you can get some idea of the megalomaniacal scale of this place...
http://jpatokal.iki.fi/photo/travel/Malaysia/Putrajaya
http://wikitravel.org/en/Putrajaya