I know this is a little late, but figured I'd throw out some more info in case other people in the future would need it.
From Seattle to Mt. Vernon, a town about 20 miles east of Anacortes, you can take Amtrak. It runs twice daily, and allows roll-on bike service for an additional $5.
Or, if ya feel like saving some money, you can take a Sound Transit commuter bus from Seattle to Everett station. From there you can hop on a Skagit Transit Route 90X bus that runs during commute hours Mon-Fri:http://www.skagittransit.org/index.cfm?pageID=36727
The riding from the Mt. Vernon Station to Anacortes is pretty straightforward. West on SR 536 then west on SR 20 across the big bridge, then after bridge/casino get onto March Point Road (the exit right after the bridge). This will go on for a couple miles, then turn right after the Park n' Ride near the coffee place. You'll come across a rail-trail that will lead straight to downtown Anacortes and then it's a few more miles on SR 20 Spur to the ferry teminal to San Juans/Vancouver Island.
You could also take Skagit Transit buses from Mt. Vernon to Anacortes if you like, though you'll have to transfer. And the bus service is limited, so timing is crucial.
Riding north out of Seattle to Anacortes isn't the most thrilling thing, as I've done it once. I used the Interurban Trail north, which varies from decent to annoying. Then I used surface roads to Mulkilteo where I caught a ferry to South Whidbey Island and then rode up the island mostly using SR 525/20.
I've never tried it, but the RSVP route brings you from Seattle to Burlington, just north of Mt. Vernon. It tracks to the east, so it's not the most direct route:http://shop.cascade.org/sites/default/files/RSVP-Route-Map-2011.pdf
Deception Pass is cool for camping. The south unit (Cranberry Lake) has hiker/biker camping spots. Watch out for the raccoons, though. (They can be a problem at many places on the coast.) North of the bridge is Bowman Bay campground (still part of Deception Pass S.P.) which I liked much better. There's no hiker-biker sites, but most spots offer a great view of the bay, and there was less noise from the nearby Naval Air Station. The drone of jets was omnipresent all night at the hiker-biker spots at Cranberry Lake.