Some people are reading way too much into this! I just thought it was pretty cool to see the mighty Wokka featuring repeatedly on primetime TV.
Be pleased that a major company with massive public exposure chooses to associate itself publicly with the RAF. You'd be complaining a lot more if they had taken some sort of anti-forces stance eg "Waitrose refuses to acknowledge armed forces in major publicity campaign". I guess some people just go looking for something to be p1ssed off about! Relax - it's nearly Christmas.
(However, it wouldn't go amiss if they sent a few pallets of Christmas dinner out to the Stan and dropped H for H a few quid. Maybe they will.)