I have a friend who wants to bike from Pflugerville (say the corner of
Heatherwilde and the Pflugerville Loop) to the Whole Foods in Gateway
Plaza. I've done this ride once or twice and can offer suggestions, but
maybe someone who lives in the area has some specific suggestions for
the best way to go without getting run over?

Here's one halfway decent possibility that I would probably take if I was
making that trip:
http://www.toporoute.com/cgi-bin/getSavedRoute.cgi?routeKey=HAUTQHUHAPVMKYX

Getting around northern Pflugerville is pretty easy, since it's almost all
residential streets. Grand Ave can be a pain, but might not be too bad on
weekends. Grand Ave does have sidewalks most of the way along this route if
you're not comfortable riding in traffic, and it's probably better than the
other I-35 crossings. Oh, and west of I-35, watch carefully for uncovered
drain-pipe holes in the road. And if you're not comfortable on Grand Ave,
here's an option for cutting through some residential areas:
http://www.toporoute.com/cgi-bin/getSavedRoute.cgi?routeKey=LERTYHVHEXFIEBU
On the map you'll see a gap between Gower St and Edgemere. There's a small
park there with a wooden pedestrian bridge across the creek that you can ride
a bike across.

Getting from Grand Ave down to Parmer is pretty easy on Wells Port, Thermal,
and Metric. They've been repaving Metric recently, and the bike lanes may
have disappeared, hopefully just temporarily. At Parmer, you could take
Parmer directly to Amhurst, which is about a 1 to 2 mile stretch. It has a
wide shoulder, although you'll probably want to take the sidewalk on the
bridge over Mopac and be very watchful at all the intersections. If you're
not comfortable on Parmer, here's an alternate route to Amhurst on
lower-traffic roads that adds a little extra distance:
http://www.toporoute.com/cgi-bin/getSavedRoute.cgi?routeKey=BFYYJGECODWDIQH

Amherst is okay, and Duval is much better (west of Amherst) now that they've
narrowed it from four lanes to three lanes and added the new bike lanes. Then
over to Balcones Woods and Jollyville, which has bike lanes. Then to Great
Hills and Stonelake and you can get into the shopping center from Stonelake
behind REI.