I find the whole TM thing pretty fascinating but without any real investment either way in whether it's legit. From what I can gather, if it's a cult it's a pretty soft one: a lot of people go to them to get a mantra and technique and then depart without any pressure to stay. On the other hand, any organization that is charging fees for spiritual teachings automatically rings alarm bells for me. My completley uninformed and therefore worthless suspicion is that most likely, the technique is effective and useful but the organization somewhat suspect as most institutions are. Not Church of Scientology-level though.
This is more or less my take, though my stance on the TM organization is a bit harsher. I learned it in India, where it wasn't insanely expensive... I cannot fathom charging the kind of money they charge in the U.S. for these teachings. They used to charge $2,500, and I believe these days it's $1,500. At those prices, I find what they do unethical. The technique on its own is actually good. Meditation is good, and TM is about the easiest form of meditation there is. The TM organization tells you not to teach anyone, because of course they want people to give them ridiculous amounts of money, but I swear I could write three paragraphs detailing the technique and give you about 75% of what you'd get forking over the money. I can't give you the mystical mantra but I don't believe the mantras they give are any more effective then any mantra you can make up. Pick a word you like and google translate it in Estonian... it'll work. I agreed not to teach it so I won't, but the book "The Relaxation Response" boils it down and gives you the gist.
I've also learned the Vipassana Meditation technique. It's far, far more difficult. For most it would be one of the most challenging undertakings of their lives. It requires a 10 day course which includes food and lodging. There's no way I could approximate what I learned there in writing or even if I were to meet you and give personal instruction. The total cost for the 10 day instruction, food and lodging? $0. Everyone who runs the course is doing so on a volunteer basis. At the end of the course, open only to people who have completed it, there is a donation table. They don't even pressure you to go up to it.
I do think Lynch's foundation is doing good work, but they make it available only to people who meet certain criteria, where as Vipassana is available to anyone. If the TM organization was really interested in helping the world with their technique, a comparison to the Vipassana organization doesn't give them much excuse for not doing it much differently.
As for whether the practicing the TM technique makes one a Hindu, it does not. There is a puja performed at the "initiation" when you learn it. This is supposed to pay respects to Maharishi's teacher, Guru Dev. A puja is certainly a religious ceremony, even if they claim it is not, but it is the only time a religious ritual is performed in the teaching of the technique. Beyond that, it is just a simple technique of meditation that can be practiced by people of any belief system, or no belief system. I don't know if Lynch considers himself a Hindu, but being a practitioner of TM does not make him one.
If I ever had the good fortune of meeting and speaking with David Lynch, I wouldn't bring any of this up because we'd have some major disagreements, and there would be plenty of things I'd rather speak to him about. My view on the TM organization has no bearing on how I view him as an artist.