The word "jihad" has a wider meaning than "holy war". It would better be translated into "worthy struggle" — with "worthy" being very subjective.
Islam is in fact the largest religion (by worshippers) in the world today, so Frank Herbert's assumption that a culture derived from it would be dominant in a future society is just extrapolation.
I think the current estimate is that there are almost a half a billion more Christians than Muslims (in 2025.)
One reason is that the number of Christians in Sub-Saharan Africa is growing. But extrapolating the trends, yes Islam will probably become the largest religion in the coming decades.
Or at least maybe - looking at birth rates, it seems as second generation muslim immigrants to Western countries have even lower birth rates than the native population. That might happen also in regions say like Pakistan and Indonesia and other fast growing regions, depending on economical or other changes.
> Islam is in fact the largest religion (by worshippers) in the world today, so Frank Herbert's assumption that a culture derived from it would be dominant in a future society is just extrapolation
Fyi,
> Dune is a 1965 epic science fiction novel by American author Frank Herber
The distinction you're making wrt Jihad is also super modern and did not apply back then