The official Pacific Coast Route between Sausalito and the Golden Gate Bridge will be closed for improvements from March 1 through June 1, 2010. See http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2010/02/27/MNDI1C63EN.DTL#ixzz0glBddeNq
Ultimately this should improve the route, but meanwhile "The closures will start Monday (3-1-2010) with East Road, which is used by many bicyclists to ride from the Golden Gate Bridge through Fort Baker, into Sausalito and back. That route will be closed to all traffic from 7 a.m. to 6 p.m. Monday through Friday until the end of May, according to Alexandra Picavet, the recreation area spokeswoman. People heading to Fort Baker should use Bunker Road, she said."
An alternate route frequently used by local cyclists is to go up Alexander Avenue and under I-80 to get to the golden Gate Bridge, instead of taking East Road (the route on the ACA maps) through Fort Baker. For the alternate route, see:http://maps.google.com/maps/ms?hl=en&ie=UTF8&msa=0&msid=103758683106284781168.000480986591b82d3a7e2&ll=37.839157,-122.480199&spn=0.016014,0.02002&z=16
It looks like this will always be open.