1. There are many types of meditation: many are a form of intense concentration, others are a witnessing or watching of thoughts, yet others are a form of profound devotion. So it is no surprise that different forms will produce different effects in the brain.
2. The fact that the brain can be trained to produce certain types of electrical activity is in line with multiple lines of evidence demonstrating that the brain is not the static structure that we used to think it to be: it can learn and develop. We already knew that with motor functions and some cognitive abilities, but now we can extend those findings into the emotions: feelings of love and empathy can be developed, expanded and deepened. The old metaphor that the brain can be exercised like a muscle may not be a metaphor after all, but a biological fact.
3. The fact that there are neurological correlates of meditation or of any emotional or psychological state does not mean that we can reduce the experience to the firing of some neurons or the synchronization of regions of the brain. Some of this research has been misinterpreted to mean that meditative states or mystical insights are no more than the calming of neural activity. It is vital that we also acknowledge the subjective experiences and reports of individuals and recognize that they are as valid descriptors as changes in the brain.
4. Meditation has been shown to have a great many physiological and psychological effects, from lowering blood pressure, to improving the performance of sleep-deprived individuals, reducing age-related cortical thinning and ultimately leading to demonstrable psychological and spiritual development. So the neurological and psychological findings provide a partial explanation for those observations.