Jay,
We keep our boat at Skyline Marina, so we're there often. There is a sling launch and parking there.
The parking isn't fenced, but we and guests have parked there for weeks at a time and have had no problems. It's a pretty quiet area compared to either Bellingham or Cap Sante.
The biggest advantage of Skyline is its close proximity to the San Juan's. Depending on which pass you take, it's 15-16 miles from Skyline to Friday Harbor. Cap Sante on the other side of Anacortes is 21-22 miles and Bellingham is 27 miles from Friday Harbor. The distance doesn't really matter if you're staying for a while, but it can make a difference on a weekend if the weather takes a turn and you want to get back.
We usually take Lopez Pass to the inner part of the San Juan's. It's less than 5 miles across Rosario Strait from Burrows Bay to the entrance to Lopez Pass. After that you are in protected waters all the way to Friday Harbor.
Bellingham is a great town, but I don't like Bellingham Bay. It's a good place for a sailboat. I don't remember a time that I was crossing it when it wasn't windy and had an uncomfortable chop.
Lyle