I've heard legends varying from "it should be optional as some small compilers should be able to be C11-compliant without VLAs" to "it was a mistake on the first place". I've never got one true and definite answer to this, though. Ultimately, I don't believe anyone really has one as the reason (assuming - and hoping - there is one) was never disclosed (as far as my old searches went).
From Chapter 4 (page 13) of Rationale for International Standard - Programming Languages - C 5.10 (2003)
By defining conforming implementations in terms of the programs they accept, the Standard leaves open the door for a broad class of extensions as part of a conforming implementation. By defining both conforming hosted and conforming freestanding implementations, the Standard recognizes the use of C to write such programs as operating systems and ROM-based applications, as well as more conventional hosted applications. Beyond this two-level scheme, no additional subsetting is defined for C, since the C89 Committee felt strongly that too many levels dilutes the effectiveness of a standard.
Emphasis mine. Notice that this decision goes against their own rationale. Yet, another thing made optional. Now you either get
__STDC_NO_VLA__ or VLA support. It is a very odd decision.