Since you've read up on Final Fantasy XI, I'm sure you've become aware of how party oriented the game is. Because of this, each job is required to have a specific role in the party. Some jobs are more flexible than others (most specifically RDM which can take on various different magic-oriented roles), but most serve a single purpose.

When it comes down to it, there's four different categories that people usually refer to: Tank, Damage Dealer, Support, and Nuke.

Tanks are most often Paladins (for their ability to build massive amounts of hate and heal themselves) or Ninjas (for their ability to create shadows to take damage for them and their high evasion). Earlier on Warrior is also a valid tank, but past level 40 most WARs will refuse to tank and instead walk the path of a damage dealer.

Damage dealers are exactly what they sound like, they're the ones that provide the main physical offense for a party. The primary damage dealers are monks, warriors, thieves, dark knights, dragoons, rangers and samurais. I'm unfamiliar with puppet master's role in a party (I've only ever partied with one once), but I can assume this is where they'd be. On the sparse occasions that BSTs party, they'd also be part of this category.

Support jobs include red mage, white mage, bard, and corsair. Their job, obviously, is to support the others. White mage and red mages are often main healers (RDM can fill in for a lack of WHM and, in my experience, often does). Bards focus on increasing the party's stats through their songs. Red mage has refresh (restores 3 MP per second for a total of 120 MP), and BRD has mage's ballad I and II (similar effect). Corsairs are very similar to bards. I've only ever partied with one, but what people most often talk about is their ability to refresh the party and the experience bonus they can provide. Summoner can also fall into a support role by taking the job of main healer. I haven't seen this much in the later levels, though.

The last group is the nukers. Black mage is the primary nuker. Basically it's just the jobs that deal out massive elemental damage. Summoners also fall under this category with their avatars' blood pacts, but only some of those are elemental in nature, while others are physical.

The selection of sub jobs are most often dependent on enhancing that job's strengths instead of making up for its weaknesses. Damage dealers usually rely on warrior or thief subjobs (warrior for strenght and thief for SATA). Thieves and warriors are often seen with ninja subs. They both use it for dual-wield (highly overrated, if you ask me) and both make use of the utsusemi: ichi/ni abilities that create shadows to take damage for you. I've seen DRK/NINs as well, but they're rather uncommon in parties as DRKs specialize in scythes and great swords (both two handed weapons). The only time I've seen that combination effective was with a DRK/NIN with full axe merits.

As for the subjobs you mentioned, Scott already addressed those. The only real advantage I can see to a DRG sub is the passive accuracy bonus, but the lack of the DRG's wyvern really hurts it as a functional sub job. Edit: I was unaware of the new developments with DRG as a sub. Probably just a phase with the haste obsession.

If you're really upset about jobs having a specific function, perhaps this game isn't for you. As far as I know, though, this kind of set-up is pretty standard in any MMO reliant on parties. There's always solo'ing for exp., but for the most part, such a thing isn't really managable in Final Fantasy XI unless you're a beastmaster.