I think you may be misunderstanding the scientific method a bit. We don’t just believe an experiment because it hasn’t been disproved. We believe an experiment because its result can be reproduced consistently. I suspect, and the article I linked to suggests (with cites), that there have in fact been other studies which have not shown a positive result for transcendental meditation having the sort of effects you describe. However, the people promoting transcendental meditation (and who stand to profit from people believing in it) are selectively reporting only those studies which back support their claims, not those which contradict them. I also suspect that if you look at who’s conducting these experiments, you’ll find that those which achieved a positive result were overwhelmingly the work of people who already believed in or were the proponents of transcendental meditation, whereas those that contradict it were not. If it were a real phenomenon, you wouldn’t expect the result of the experiments to be correlated with what the experimenters believed. I suspect that the investigators are either conducting biased experiments or simply not reporting those results which contradict their hypothesis. (See cites in the skepdic article for some support of this.)
Here’s why you can’t just judge an experiment on whether or not it has been disproved: even if the experiment is biased, it may not be possible to identify the source of bias (unless you could travel back in time and examine the conditions under which the experiment was conducted). If I simply omit some information about the experimental procedures (or give false information), then the source of bias in my experiment will be concealed. But if the experiment can’t be duplicated by independent, unbiased researchers, then it’s a good bet they did something wrong. (Even so, many of the experiments the TM promoters are touting have been shown to be biased – TM promoters just fail to mention this, and deny it when it’s brought up.)
You might think you “believe in evidence” and that I’m a “closed minded skeptic”, but the fact is that the evidence for TM having these effects is really quite lacking, despite what TM promoters might claim. It’s easy to produce biased studies to support just about any conclusion, and the promoters of TM have a strong financial incentive to do so. Furthermore, my skepticism is, I think, well justified. The TM promoters claim to observe phenomena with no known physical cause, and then go on to claim they know how these things work, and offer an explanation based on pseudoscience like “higher states of consciousness”. What percent of neurologists do you think believe in “higher states of consciousness” of the sort Maharishi Mahesh Yogi describes? It would be one thing if he were saying “I think this works, but I can’t explain it.” But he says he can explain it. Modern science doesn’t know everything, but do you really think it likely that this man knows so much more than scientists who have devoted their whole life to the study of the brain, using the most advanced techniques available to us? That doesn’t make you the least bit skeptical? I ask you, which is more likely: that he spent a couple years in meditation and suddenly discovered some hidden secret of the universe, or that he saw an opportunity to get rich by telling lies?
If you’re really “open minded”, you should search for and read some of the literature claiming transcendental meditation is a fraud, and weigh those claims against those of the TM promoters to see which seems more plausible. (You can start with the stuff linked to from that skepdic page.) But it sounds like you’ve instead chosen to assume that the TM promoters are telling you the truth, despite their obvious incentive to lie to you. It’s one thing to be open minded – to consider all the claims put to you fairly. Another thing to assume that people are telling you the truth, and to trust extreme claims without going over the evidence with a fine-toothed comb, listening to the criticism of those claims, and seeing if it really holds water. Skepticism doesn’t mean closing your mind to possiblities, it means demanding extreme proof for extreme claims. Unless you have strong reasons to believe the studies aren’t dishonest, biased, or otherwise flawed, 50 studies or a million doesn’t amount to extreme proof.