To protect a wood deck, remember: wood is organic. It lived and breathed. The tissue it developed is an extension of the natural world, which is susceptible to decomposition and decay. 
Not to be a downer, but you, yourself, are no different. You take care of your skin to protect it from the sun and to regulate its moisture.
The wood in a deck is no exception to this fundamental concept. 
How then does preserved wood stay whole while household wood products wither away if not given the right attention? The difference is a matter of protecting it from the elements. 
First, let's think about the root cause. No pun intended.

What Will Cause Wood to Deteriorate

The sun, specifically ultraviolet light, will strip color from a deck. A combination of water, temperature, and oxygen will lead to wood rot. It's fungi that causes wood to deteriorate. They attack it and feed on it. 
"When the spores of fungi fall on a suitable medium under moist conditions they germinate somewhat in the manner of seeds. The spore wall bursts and a minute tube, called a hypha, grows forth. The hypha branches and the tiny tubes begin to permeate the soil, compost or wood medium on which the hyphae are growing. With wood-rotting fungi the hyphae spread through the wood, disintegrating the cell walls and reducing their strength," according to a paper published by Canadian Building Digest in 1969.
The cell walls are usually dissolved by fungi in order to be consumed. This subtle, slow-going degradation in the wood will cause structural damage and soon critical decay.
The fungi work their way into the wood and aren't just a surface issue. It's not just a matter of scrubbing the exterior and calling it a day. Though, we'd all like it to be that easy. No, the pores of the wood must be secured, sealed, and kept away from the damaging presence of foreign bodies and sunlight that would otherwise break down the organic matter. Another thing that can help is applying wood borate to kill off insects and fungi.
Once damaged, wood fiber will separate (or be consumed) from the underlying cells. Later, bacteria and insects can make their home within your deck. No one wants that.
So, the key takeaway: water will be the primary issue you need to thwart, alongside sunlight.

How Does a Stain Prevent Wood Decay, and Which to Choose

Well, there are different types of stains and choosing the right stain isn't always easy. 
An exterior penetrating stain will soak into the wood after it's coated. Some include a mildewcide. Others may include UV light absorption. They're available in water and oil-based solutions.
In a typical pigment-based wood stain, there's a colorant that's suspended in solvent with a binder. The solvent is a liquid, the colorant is exactly what you think it is (something that colors a substrate), and the binder acts like a glue to adhere an oil-based pigment to the surface. This binder will act as a layer of protection, and with multiple coats will yield a seasonal barrier against unfavorable conditions and moisture. 
A stain-sealant combo is a solid combination to choose when deciding on the best stain to protect a wood deck — this could be integrated as one quick-to-use formula, or it could be a separate stain job and sealing job with a polyurethane finish. 
A common method of sealing wood against moisture is a film-forming sealant. They bond to the surface (or substrate) and provide a glossy, shell-like exterior that can also contain oil or water-based colorant. A marine varnish is a go-to for sealing exterior wood, often containing UV-blocking substances as an extra layer of defense. Though, it will take multiple coats to gain an appreciable level of protection against sunlight. 
Oil stains dry and solidify in one solution, so to speak, yielding a bit more protection than generalized water dyes. Though, water dyes can be quick-to-dry, low-odor, and less expensive. 
How you choose to spend your time and resources is up to you. Maybe this all sounds like too much work, but chances are high that you're willing to put in the time, money, and effort to protect the property you spent so much on. 
The end product you choose is also up to you. A stain-sealant combination or an oil-based stain is a good choice that many rely on, but keep in mind that it's not a one-and-done matter. There will be consistent maintenance and upkeep.