While products like Tyvek do act as a drain plane to some extent, they're not truly waterproof. They're designed to allow vapor to easily pass, and therefore they're inherently an imperfect waterproofer. They should be considered a second line of defense against flawed siding installation and occasional wind-blown water intrusion.
The flashing around windows and other penetrations has as much to do with stopping airflow as it does with stopping water. Housewrap is mostly concerned with air leakage, which can dramatically affect the energy efficiency of a building's envelope.
The bottom line is that nails in the field are less likely to be subject to water on a regular basis, and they do somewhat self-seal. Window flashing is much better at self-sealing and is used in high-risk areas. Housewrap should not be considered a substitute for proper siding drain planning. Steel and vinyl siding channels, for example, must lap properly in order to direct the flow of water outside the siding.