This answer is a little more general than you're probably looking for (it applies to all web apps, whether Flash/Flex-based or HTML/CSS/JS based or whatever), but...
It depends a lot on the use case for your application. Is it an application that will be loaded all day and pull in updates as necessary (like Gmail) or is it something that will be launched, used, then closed?
If the former, besides reducing resource size, you are probably alright here. It makes more sense to get the downloading all out of the way at once, rather than to expect the user to tolerate delays at every turn.
If the latter, you should lazy-load as much as possible. In other words, for example, instead of embedding all of the application's graphics into the SWF, load them with URLRequest
s or whatever method necessary when they are needed. A quicker launch will "feel" faster and more than make up for the increased HTTP requests over a short time.