Like any big city, you'll find lots of options for accommodations in San Francisco. You didn't mention your budget, but there are motels, hotels and AirBnBs that will fit whatever your price range.
Since you mentioned that you'll be on your honeymoon, I'd strongly recommend the Inn at the Presidio. The Inn is located in newly restored and renovated turn-of-the-century buildings situated in the Presidio, which is part of the Golden Gate National Recreation Area. It's a bit pricey, but I don't think you'll find a more romantic and unique stay anywhere else in the city. (Honestly, if you were to come to San Francisco right now, the skyline is filled with construction cranes and there seems to be roadwork on every other block in downtown.) The Presidio is truly beautiful, and offers acres of open nature, miles of hiking and biking trails, breathtaking views of the Bay -- including the Golden Gate Bridge and Alcatraz, and feels like a place out of time and away from the hustle and bustle of the city.
Staying in the Presidio also easily checks off two of your top three attractions. The Walt Disney Family Museum is also in the Presidio and is less than a 10 minute walk from the Inn. You'll have wonderful views of the Golden Gate Bridge almost anywhere in the Presidio, and it's maybe a 30 minute walk to any number of vista points for the Bridge, including Chrissy Field, Fort Point, or the Golden Gate Bridge Pavilion. You could even go further and walk across the Bridge, or you could rent bikes from a vendor in Chrissy Field or the Sports Basement and ride around the area and across the bridge.
I'd agree with the suggestions that you shouldn't need a car -- unless you plan on traveling out of the city. Parking can be difficult to find and expensive in San Francisco. You can call a taxi or hail a ride share car when you need one. Both Uber and Lyft are headquartered here and you'll have no problem hailing a ride through these apps. The Presidio is a bit isolated from the touristy areas of Fisherman's Wharf, Pier 39 (where you'd catch a ferry to Alcatraz), and Union Square, but San Francisco is a compact city, and traffic depending you're not much more than 15 minutes away from any of those neighborhoods.
Good luck!