Alexandria Church Bombing
One is the way it has highlighted Coptic alienation from and lack of faith in Muslim society and the Mubarak regime, as seen in the sometimes violent protests. Paul Schemm provides an excellent background on that issue. Juan Cole notes that Muslim leaders, and for that matter many non-leader Muslims, have condemned and bombing and joined in some protests, but there definitely seems to have been a quiet pattern of social transformation leading to Copts feeling their minority status more acutely.
Another is its possible connection to the al-Qaeda-inspired Islamic State of Iraq's new anti-Christian campaign which they justify in part by referencing those tensions between Copts and Muslims in Egypt. The investigation is focusing on Iraq links, though Issandr El Amrani believes that the perpetrators were probably Egyptian. Juan Cole believes they may have been foreigners, though he also credits the possibility of a new group within Egypt, probably of only a single cell, as mentioned by Issandr.
The third angle that seems worth mentioning is how this might harm the legitimacy of the regime as it prepares for a transition in power. Having a violent sectarian clash can't be good, and may give the government incentive to move decisively and in a high-profile way against somebody or other to try and calm the internal situation and show it can still provide security.