It really just depends on how much they like getting billions in aid from the US. If they aren't pro-Israel, they won't be getting nearly as much and without the aid, it's unlikely the new government will be able to sustain itself. This is especially true if it's a secular government.
Let's hope you're right about the effects. But the US annual aid to Egypt totalled about 1.5 billion $ in 2010, with 1.3 billion $ of it in military and security assistance. These figures do sound to me like too small to be a make-or-break deal for an egyptian government.
According to
this article from 2009, it might currently indeed be too small to make a difference, at least for the ordinary egyptian:
With U.S. economic aid to Egypt cut to $200 million for 2009, the per capita share is a measly $2.60 in a country with an average gross domestic income (GDP) per capita at current prices of about $1,697 in 2007 and $2,184 in 2008 according to the World Development Report of 2009—the sharp increase is partially attributed to the high inflation rate of 11.8 percent in 2008. If calculated using Purchasing Power Parity (PPP) that adjusts for the relative purchasing power difference between the Egyptian pound and the dollar, the average per capita income in Egypt was $5,352 in 2007 and $5,400 in 2008. Therefore, in per capita terms, U.S. economic aid to Egypt is barely a drop in the bucket.
edit: Personally, I believe the military represents the best hope for an orderly transition and a favorable post-election situation in Egypt and the region. After the removal of Mubarak and his inner circle, the egyptian military is one of the few remaining pro-US/pro-Israel factions of significance left in Egypt. But I am a bit worried about the Muslim Brotherhood, which is arguably the best organised political force in Egypt, hostile to Israel, and pro-Hamas. Even if things work out in the interim and the elections roll out in September, it is hardly unheard-of in the region for masses of poor people without democratic traditions to "vote wrong". It takes a long time (and some would say a large, strong, and politically aware middle-class) to build such traditions, whilst the democratic process can be subverted in a couple of election cycles.
I'm not saying that the military should take over permanently, mind you. Just that they will be the most crucial factor in the development of a favorable long-term political outcome in the country, IMHO.
