I have a similar bike storage issue: I want to keep my bike at the front of my flat (=appartment), so that I can get on it when I go out on to the street, without having to carry it up stairs, or down a muddy lane from the back yard. Weather, rust and theft are concerns, but so is speed and convenience in getting going every morning.
We have a Cycle Hoop bike hanger in our street, which is great for security and weather protection, but it has a rental cost, and takes time to walk to and open and close.
Similar to amcnabb's answer, I tried commercial bike covers, but found them flimsy and hard to store when not in use. I've similarly found a decent solution using tarpaulin.
I have a solid iron fence in front of my flat, and so lock my bicycle to this, and then cover it with a rectangular section of heavy truck tarpaulin (free from a car scrap yard). This works well for weather-proofing, especially if air vents are left, but it is still a hassle to get off the bike in the morning.
By adding 20mm galvanized pipe horizontally, and a handle, lifting this cover becomes much quicker, and run-off water can be directed away from one's clothing. The ends are left open this way: in practice this allows air-flow, thereby reducing condesation, and rain doesn't get much past the tyres: important areas like handlebars, transmission and saddle stay dry. The pipe helps to keep the tarp weighted down. A pocket can be added in the tarp to accommodate the handlebars, jointed using eyelets and stainless bolts or otherwise.
The result provides a decent combination of weather protection and therefore protection from rust and decay; and also convenience. Security comes from hiding the bike from immediate sight, but primarily from a very solid lock (motorcycle chain) left permanently under the cover, but small chain-and-padlock locks can be added at the front and back to lock the wheels - and keep the cover down in case of storms. The cover is easy to leave in place when you use the bike. It depends though on having a fence or similar permanent fixture to mount on or over; and there is still clearly some risk of targeted theft when a bike is regularly left in same place outdoors. I'm happy to store my town (commuting) bike like this, but a more valuable (and less often used) one stays indoors.
The idea and its use is somewhat documented at bikehide.org. Disclaimer: I designed this myself and have produced a few for friends: it isn't commercialized (yet, at least!).