EDIT: Hacker news won't let me respond, but the answers below all seem to be because the original meaning has been lost on everyone.
In English, the word 'kernel' means 'core'. An OS kernel is the core of an operating system. In linear algebra, the kernel of a matrix (or a linear transformation, same thing) is the set of vectors it maps to zero, which is also in a sense the 'core' of the mapping (in so far that zero can be seen to be at the 'core' of the vector space / number line).
So actually, the definition is the same, it's just that the word kernel is rather rare, despite having a well understood meaning. Nevertheless, it is the kernel of many common English idioms such as a 'kernel of truth'.
Going to ML kernels... the etymology is a bit convoluted. I believe they come from operator theory and support vector machines. But nevertheless, the 'normal' meaning of kernel works out because kernels are typically the core fundamental operations supported by a machine learning framework atop which the other operations are built. In that sense, regardless of the etymology, the name actually fits.