I think that the Nile Cruise is sort of a part of the Egypt travel experience.
You can find many through packaged tours or by turning up last minute - likely much more supply than demand these days.
I was last in Egypt in May 2011. I didn't have any issues with security, although there were unscheduled evening protests happing around Tahrir in the evenings.
I don't think you'll have any trouble, unless you decide to go looking for it.