The first is that the same Mubarak regime which has held generally good relations with Israel is the same regime which did very little about the anti-Israel views of the Egyptian public. It's no accident that Mein Kampf and Protocols of the Elders of Zion is available at book kiosks in Egypt, while the anti-Mubarak newspaper Addustour is often censored. The regime's policies work in Israel's favor, but certainly not because it is a fan of Israel.
Which leads to the second point. Egypt and Israel collaborate based on a confluence of strategic interests, not because they like each other. Both Egypt and Israel have stated an interest in containing Hamas, and maintaining security in the Sinai. These interests are the basis of Egypt's foreign policy. While the tenor of domestic politics will almost certainly change if Mubarak is unseated, Egypt's foreign policy interests will not. This is not to say that policymakers should "black-box" Egypt and consider its domestic politics irrelevant (just ask these really smart political scientists). However, if Egypt's foreign policy interests are held stable, domestic changes are only likely to affect foreign policy within a certain order of magnitude.
There can be little doubt that relations between Israel and Egypt are likely to take a turn for the worse in the coming weeks and months. However, policymakers must seek to understand as accurately as possible what this change will look like as they quickly respond to developments in Egypt. Relations will deteriorate, but any assessment that this deterioration will be catastrophic is likely an overstatement.