I usually keep a low profile here because I'm a lowly private pilot. That said, I've worked on embedded computer systems for the last 20 years and I do know something about them.
The Actel issue revolves around securing the custom programming in their field-programmable gate array chips. These chips are purchased from the manufacturer as blanks and are then programmed to implement complex logic functions. The programming itself requires attached equipment and a development environment of some sort. Although it could be done, reprogramming these parts is virtually never possible through network connections. The real issue here is not the possibility of the chips being maliciously modified, but the possibility of a competitor reading out the programming and duplicating them. The manufacturer claimed that the programmed data was encrypted and impossible to read out and a researcher claims that it is possible to get it out.
I'd also point out that most avionics have flash memory chips that are not encrypted and much easier to read out and reprogram than an Actel FPGA chip. Assuming an intruder had access to the avionics bay and wanted to cause trouble, this would be a much simpler approach.