Even in the article you cite, it questions how big a bubble the "tulip mania" really was. How does any existing government structure limit how much I want my Pokemon, or Care Bear or Cabbage Patch doll, and how much I'm willing to throw at it? Those are speculative bubbles just the same, and some people take a hit from them, and some people don't. Should the government somehow prevent those?
And how long did it take society to recover from the bubbles before the government started intervening? Typically not very long. Do you think tulip mania caused a great depression in Holland?
What does lowering interest rates do? It makes more money available, to be applied to less-valuable or more risky ventures. (i.e. if you only have a small amount of capital, you'll be cautious were you spend it, and you'll spend it where you'll minimize risk and maximize reward. If you have a second small amount of capital, you'll use that on the next best, and so on.) We should be raising interest rates, to reduce the amount of risk we're taking on as a society.
What about subsidies? The government is a giant layer of "management". Any dollar that's funneled through it, gets a large hunk shaved off, before it's spent on anything. And in order to get that dollar, the government either has to take it from someone else who'd be perfectly happy to invest it or spend it, or it needs to take it in the form of a loan. The loan is just taking it from a citizen later on, and with interest. Again someone who'd much rather have that dollar, and spend it or invest it themselves.
Given the recent situation, should the government have let the banks collapse? I don't know. Should the gov't have let the automakers collapse? Absolutely (and helped other companies purchase the assets, smoothly, and helped with retraining).
Never trust an operating system.