I'm sure that the German government provides travel advice for its citizens, however I couldn't find any in the English section of the federal foreign office's website. The German language advice on Egypt can be found here (thanks @simbabque, who indicates it gives similar advice to the UK's FCO).
The UK's foreign office does however proide a fairly detailed page of advice on Egypt. They note that
There is a high threat from terrorism.
Over 900,000 British nationals visit Egypt every year. Most visits are trouble-free.
There is blanket advice against travel to North Sinai at all, and advice against "all but essential travel" to the rest of Sinai and any of the western desert regions. However, none of the areas you mention visitng are in these areas. The fortified areas of Hurgada and Sharm El Sheikh are mentioned as being especially secure, althogh flying to or from Sharm is advised against. (The question remains as to why the FCO feels that other Egyptian airports are safer, as one would expect similar security measures at all of them. Perhaps there are specific issues at Sharm el Sheik).
Edit: The Egyptian government has just claimed (after this answer was placed) that there is no evidence of terrorist involvement in the recent plane crash.
Beyond issues of terrorism and violence, the FCO draws particular attention to dangerous conditions on the roads, saying that
Accidents are common, mainly due to poor road conditions, dangerous driving and non-enforcement of traffic laws. The UN estimates that road accidents killed almost 16,000 people in Egypt in 2011.
and that many incidents have occured on Nile Cruises:
River and sea travel
In the past, overcrowding and poor safety standards have led to several accidents on Red Sea ferries and Nile cruisers. There were four significant fires on Nile cruisers between September 2006 and November 2012.
So it would seem prudent to enquire with your travel organisers as to the standards that they hold your vehicle operators to.
Is this safe enough for you? That is a personal value judgement, but the UK's authorities at least are not stating that what you wish to do is something that is necessarily avoided.