Cooldowns are a limiting factor of supply. Economically, some items can't be available with virtually infinite supply, or else the items they can be made into would become cheap, and therefore less valuable, in the eye of the average player. Part of what Blizzard does (extremely well, in my opinion) is balance what players want with what they think they want.
You can't always get what you want ...
How much fun would it be to play WoW with cheat codes? Aside from the initial fun you'd have breaking all the old rules, how much time would you actually spend playing the game if you could make everything without working? Items would lose their value from your perspective, because you could simply make whatever suited your current wants the most. The value of an item is defined by its desirability to players, and scarcity is an important part of the equation our minds calculate when we're comparing two items.
You see where this is going? One of the most long-standing design principles in WoW is that while you may be able to get a couple of cool items with professions or gold, the truly valuable objects are the ones that can't easily be bought. There are ways around this with the GDKP system and raid teams that are willing to sell achievement runs; however, these are infrequent enough that Blizzard hasn't yet taken any steps to prevent them. Basically, though, the larger proportion of the game that is somehow supply-constrained, the more we seem to enjoy it and value the rewards we get for playing it.
All that said, cooldowns are only one way of limiting supply, and they only limit supply on commodities. Right now, you're not going to find many alchemists transmuting iron to gold, unless they're unable to transmute something like an epic gem. Still, there's nothing you can make from truesilver now that would break the endgame raiding balance, so why can't we transmute it all day long?
... but if you try sometimes you just might find you get what you need
The answer might simply be that the devs simply didn't think of it; however, I suspect the limits exist partly to protect low-level miners. Gold and truesilver are both in rather short supply and are a mainstay for low-level miners trying to make money while leveling. Still, there are a ton of new items we'll be interested in making while leveling trade skills through Cataclysm, now that epics will provide us the possibility of more than one skill-up. This demand will only add to the not inconsiderable demand already there for old world mats like gold and truesilver.
Honestly, low-level miners don't make a huge amount off really rare ores like this anyway, and if they were able to sell their other more common (and easier to mine) ores like iron and mithril to people looking to transmute them into these high-demand leveling mats, they'd probably end up better off than simply being able to sell goods from rare veins for more than they currently do.
Also, while Blizzard tends to choose the path of fewer changes on the live realms with its usually conservative patch notes, all bets are off for the next expansion. I'd be completely unsurprised if we found that the transmute cooldowns only slowed down production of the current endgame tradeskill items.
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