Popularity doesn't mean much to me. If it did, then Justin Bieber would be the highest quality band in the past 25 years, and McDonalds would be the highest quality food.
So far, I've had very good luck with Fords. They are not perfect, but I have yet to be left stranded by either of my F-150s, and so far, the most expensive repair I've had to do was get new spark plugs and coils on my old one as it was over the six digit mile time. However, I'm sure there are plenty of Chevy and Dodge owners who say the same things about their rides.
As for why Fords are a target for thieves, I can probably guess -- until 2011, the PATS system hasn't had any major changes for 5-6 years, so I'm sure there was some way to guess codes. 2011 came around with "SA" 80-bit encrypted chips compared to the previous "S" 40-bit chips. This made guessing keys a lot harder. 2013 has new physical bitting of keys -- Ford keys are "laser-cut" like Honda keys now, as opposed to using the same keyway as they have for 20+ years previously.
On one hand, engine anti-theft systems have to be kept updated to keep ahead of the thieves (such as the thieves who use two part antennas to make the vehicle think the key is nearby or in the ignition.) On the other hand, too complex makes it a hair puller and makes things unpopular (Mercedes DAS for example where if one loses too many keys, a chunk of the vehicle's computer has to be replaced for big bucks.)