By no means am I meaning any praise on the despicable person or persons involved, but this was the perfect day to do something like this. To the uninitiated, the Boston Marathon is held on Patriot's Day (a state holiday) and it more or less shuts down the city. Traffic is re-routed along the entire marathon route and public transportation is a must. Add in the fact that an 11 AM Red Sox game is part of the tradition and you now have 10s of thousands of people in a public area that's very difficult to secure.
In terms of how this effects Disney, I suspect that it means that true nighttime entertainment at Downtown Disney is less likely. There were rumors a while back about a World of Color type show - something like this would be a large draw with no entry fee.
Unfortunately extremists/terrorists/evil will look to exploit areas of weakness, so we as a society need to identify these areas of weakness before they do. I know Disney takes security very seriously, and I know it's more than just the facade that we see (bag checks). Yes, it could happen in Disney, but I would certainly feel more safe there than I would at pretty much any other public venue.