I make a distinction between yoga and Vedic spiritual practice,and I don’t mean just western style yoga. Indian philosophy is not a single homogenous whole, but is a composite of different and sometimes conflicting traditions and practices. Patanjali’s Yoga Sutras, for example, makes no mention of Kundalini. However Kundalini is prominent in the Upanishads, which is the source of the Vedic spiritual practices.
The Vedic literature is very rich, and Kundalini in particular is appealing to many because of its mystical and mysterious nature. Unfortunately most westerners don’t understand it very well, and when people fool around with things that they don’t understand, you often wind up with a lot of misinformation and confusion.
It is entirely possible to practice yoga and meditation without engaging in spiritual practices that you don’t understand. A great many people do this without suffering any ill effects, with the exception of the strained muscle here and there. The vast majority of the evidence indicates that there is nothing to fear. For a yoga practice that includes meditation, I recommend following the eight limbs as described in Patanjali’s Yoga Sutras, which avoids getting into chakras and kundalini.