I can totally understand why some people would be uncomfortable with the chanting. Once, when I was serving as a manager at a course, a student requested to speak to the assistant teacher. So I brought him to the AT and I heard him telling the teacher, 'Goenka's chanting... it's very irritating!'
The 'standard' answer to your question (that Goenka gives himself) is that the chanting is just a means for the teacher to generate the so-called 'good vibrations' for a conducive environment for practice. However, I can see how some people may not be satisfied with this answer. To be honest, if pressed further I can't say for sure if chanting does produce 'good vibrations' or not--although anthropological and/or scientific research into the functions of chanting would seem to support this.
I personally like the chanting and find it useful in helping me 'get in the zone'. Even though it has a certain ritualism to it, I don't see it as inherently 'religious'. I would draw a comparison with other 'ritualistic' activities that we are familiar with in everyday non-religious contexts. Take for example, a musical recital at a non-religious event like, say, the inauguration of a president. Before the president is sworn into office, there is usually a reading of poetry or a short musical performance (as was indeed the case with the inauguration of President Obama). These activities are performed at other events as well like the start of a major conference, start of the Olympics, even at non-religious funerals and weddings.
Now, the way I look at it, these events do not strictly require
these 'ritualistic' activities. These 'ritualistic' activities serve a symbolic purpose. But this symbolic purpose, although not measurable or quantifiable, is an important (and even indispensable) part of those events. I can't imagine not having these activities at a wedding, a funeral, an inauguration of a president, and so forth. When we listen to and/or watch these activities, we feel part of the event, we are brought 'into the zone', so to speak. I'd even say that these activities help to 'set the vibe
But of course just as some people may not appreciate certain poetry or musical recital ('don't feel the vibe', they might say), so too would some people not appreciate Goenka's chanting.
This is how I would explain the chanting to new students anyway.