The main angle this article seems to take is that this surveillance is unfair because it may target Muslims. I see no problem with surveilling the mosque of two people who just committed a terrorist attack, in fact it would be risky not to do so.
The article also points out that FBI flights circled other muslim communities as well. However all of these attacks are perpetrated in the name of Islam (albeit bastardised Islam), so it seems reasonable for them to do this, even if politically incorrect. Also, we don't know if there were any suspects in those communities linked to the attackers.
