As per Page 305, Monster Manual always doesn't mean always:
Always: The creature is born with the indicated alignment. The creature may have a hereditary predisposition to the alignment or come from a plane that predetermines it. It is possible for individuals to change alignment, but such individuals are either unique or rare exceptions.
So the question ought to be why do most dragons stick with their original alignment given the lack of planar predetermination.
The answer is part of the quote "hereditary predisposition" is the closest thing to genes you'll find in an rpg. It's in their genes.
At this point the question becomes why is it in their genes? This could mean why did the game designers create genetic predispositions regarding alignment? Or why would it be so in-game?
Let's start with a definition:
Wikipedia on "Dragon (Dungeons & Dragons)" (emphasis added)
In D&D, dragons are depicted as any of various species of large,
intelligent, magical, reptilian beasts, each typically defined by a
combination of their demeanor and either the color of their scales or
their elemental affinity.
- Wikipedia referenced the Draconomicon (Wizards of the Coast, 2003) by Collins, Andy, Skip Williams, and James Wyatt - which I haven't read myself.
So Dragons are designed to be somewhat like reptiles. According to neuroscience and evolutionary biology the reptilian brain is very old and primal, explaining why reptiles are largely instinct driven creatures. Now dragons are also described as intelligent, which has many meanings in psychology.
According to the D&D System Reference Document it means
Intelligence determines how well your character learns and reasons.
Mechanically this covers number of languages spoken, skill points per level and modifiers to the following skill checks: Appraise, Craft, Decipher Script, Disable Device, Forgery, Knowledge, Search, and Spellcraft.
None of these demand existence of free choice, as a really "smart" robot could do any of these things. If dragons are genetically predisposed the same way a computer is logically predetermined, reasoning logically might convince a dragon to change his behavior, but never underestimate a smart mind's capability to rationalize the status quot. (See social psychology research on cognitive dissonance)
So Dragons are born with a strong drive to behave in certain ways, and are equipped with the mental capacities to rationalize to maintain that way. However, some experience the exceptional circumstances necessary to drive them to change.
I don't know the average age of dragons, but adults are about a century old and the older they get the more powerful they get, and more power makes it less likely to encounter a situation in which one's tools are no longer enough, thus normally they lack a necessity for change.