Protection will stack on different armor pieces, and provides comprehensive protection against all forms of damage except The Void and server kill commands. It is true that falling, fire, lava, poison, and even mob damage will be reduced, but false that the armor durability will always reduce more than normal. When falling off a building with Protection IV boots, the boots will not suffer any damage, producing the same results as feather falling III boots. The Armor will take more damage from Mobs and Players however.
It is possible to get feather falling IV AND protection IV boots, reducing fall damage immensely. All other pieces of armor with protection will add additional damage reduction in the same way the boots would. Protection appears to be one step down from specific defenses (ex: Protection III = Feather Falling II when taking fall damage, or Protection III = Fire Protection II when in lava).
TL;DR- Protection enchantments are slightly less effective than specific ones, but protect against everything at once. The best possible armor would be:
Helmet: Respiration III, Aqua Affinity I, Protection IV, Thorns III
Chest and legs: Protection IV, Thorns III
Boots: Protection IV, Feather Falling IV, Thorns III
Note that Only highest Level of Thorns take effect if present on multiple peices of armor. Source
First note that the Enchanting page on the wiki says that Protection, Fire Protection, Blast Protection, and Projectile Protection are all mutually exclusive, but it looks like you can have Feather Falling on boots with one of the other enchantments.
The Armor page linked in the question has a table of "Enchantment Protection Factors" provided by each enchantment. I have duplicated the relevant parts of the table below:
Since increasing the level of the enchantment only increases the EPF, when trying to find the "best" protection it is only worth looking at the highest level enchantment. The article also says that in order to maximize protection from a particular kind of damage, you would need 25 points of protection for that damage type.
Since there are 3 different types of damage, one would need 75 effective points of protection, but since each armor can add either up to 11 points to one type of protection or 5 points to each type (which is like adding 15 total), the max is 60 effective points of protection. So, you can't max out everything. And plain Protection can't be maxed out at all. Therefore, the best armor depends on what you are looking for:
If you want to maximize the minimum protection value:
Put Protection IV on each piece of armor. This will give you 20 points in every type of protection. As a side bonus, if you put any level of Feather Falling on the boots, you will max out fall damage protection.
- Protection EPF: 20
- Fire EPF: 20
- Blast EPF: 20
- Projectile EPF: 20
- Feather Falling EPF: 38 (capped to 25)
If you want to maximize the average of protection values:
Again, put Protection IV on each piece of armor. Adding Protection IV to a piece of armor adds 5 to each protection type, so it adds 5 to the average. Adding any other protection enchantment adds at most 11/3<5 EPF on average.
- Protection EPF: 20
- Fire EPF: 20
- Blast EPF: 20
- Projectile EPF: 20
- Feather Falling EPF: 38 (capped to 25)
If you want to prioritize a particular protection type:
Plain old Protection:
Put Protection IV on all 4 pieces of armor.
- Protection EPF: 20
- Fire EPF: 20
- Blast EPF: 20
- Projectile EPF: 20
- Feather Falling EPF: 38 (capped to 25)
Projectile Protection then Blast Protection:
Put Projectile Protection IV on two pieces of armor, Blast Protection IV on one piece of armor, and Protection IV on the last piece of armor.
- Protection EPF: 5
- Fire EPF: 5
- Blast EPF: 16
- Projectile EPF: 27 (capped to 25)
- Feather Falling: 23
Projectile Protection, then Fire Protection:
Put Projectile Protection IV on two pieces of armor, Fire Protection IV on one piece of armor, and Protection IV on the last piece of armor.
- Protection EPF: 5
- Fire EPF: 14
- Blast EPF: 5
- Projectile EPF: 27 (capped to 25)
- Feather Falling: 23
Blast Protection then Projectile Protection:
Put Blast Protection IV on two pieces of armor, Projectile Protection IV on one piece of armor, and Protection IV on the last piece of armor.
- Protection EPF: 5
- Fire EPF: 5
- Blast EPF: 27 (capped to 25)
- Projectile EPF: 16
- Feather Falling: 23
Blast Protection then Fire Protection:
Put Blast Protection IV on two pieces of armor, Fire Protection IV on one piece of armor, and Protection IV on the last piece of armor.
- Protection EPF: 5
- Fire EPF: 14
- Blast EPF: 27 (capped to 25)
- Projectile EPF: 5
- Feather Falling: 23
Fire Protection, then the other two
Put Fire Protection IV on 2 pieces of armor and Protection IV on two pieces of armor.
- Protection EPF: 10
- Fire EPF: 28 (capped to 25)
- Blast EPF: 10
- Projectile EPF: 10
- Feather Falling: 28 (capped to 25)
Fire Protection then Projectile Protection:
Put Fire Protection IV on 3 pieces of armor and Projectile Protection IV on one piece of armor.
- Protection EPF: 10
- Fire EPF: 27 (capped to 25)
- Blast EPF: 0
- Projectile EPF: 11
- Feather Falling: 18
Fire Protection then Blast Protection:
Put Fire Protection IV on 3 pieces of armor and Blast Protection IV on one piece of armor.
- Protection EPF: 0
- Fire EPF: 27 (capped to 25)
- Blast EPF: 11
- Projectile EPF: 0
- Feather Falling: 18
Best Answer
If you have a full set of Fire Protect IV Armor what will give you an Enchantment Protection Factor factor of 25 (9 EPF per-piece * 4, capped at 25). This should block 100% of the fire damage you may receive. Since the EPF is capped at 25, having 4 pieces is essentially a waste. It only takes three pieces of armor with Fire Protect IV to cap your EPF against fire. So you should put something else on that fourth piece of armor.
If you have a full set of Protect IV, that means your EPF will be 20 (5 EPF per piece). This will cut the damage you take by 80%.
See: http://www.minecraftwiki.net/wiki/Armor#Enchantments