Mortensen is citing two sources that say the Patriots "could move [to Jimmy Garoppolo] 'sooner than later,'" but no source would say it would happen during the 2014 season. And it shouldn't- Bill Belichick thinks the idea that moving on from Brady at this point is laughable and you should, too.
Brady is currently on an extremely cheap contract (ranks 16th in the league) and with cap space increasing, that's an extraordinary bargain. His contract is built so if he's on the team for Week 17 of this season, then the next three years on his deal are fully guaranteed. If the Patriots are in contention (and I don't see why they wouldn't be), he'll obviously be on the roster and he'll be signed up for the next three seasons.
With those guarantees, it means that any movement of Brady would involve tremendous dead space in the salary cap (upwards of $18 million bullet payment in 2015 if moved prior to June 1st, 2015, or split across two seasons if moved after June 1st, 2015; if he's cut before June 1st, 2016, there will be $12 million dead money.). There's no chance the Patriots would be willing to take on that dead money, which means he's on the team through at least the June 1st, 2016, barring a major event.
Mort goes on to cite Brady's frustration being linked to the loss of offensive line coach Dante Scarnecchia- and I'm sure Brady's a big enough person to understand that a coach retiring is no one's fault- as well as the trade of Logan Mankins, and how the weak offensive line has impacted the playcalling.
The movement of Mankins is understandable; Brady has a great connection with Mankins and they've been teammates for a decade. The move also left the team with a huge hole on the offensive line. Mort links Brady's frustration with the playcalling to the offensive line's inability to sustain itself for extended periods of time. This prevents Brady from being able to audible, or allow plays to develop in the pocket.
All of these frustrations are completely reasonable, but if Brady weren't frustrated there would be something wrong. Any human being that is used to a certain high level of experience, that is forced into a lower quality situation will obviously become frustrated by the difference. But don't read it to mean that the "tension" between Brady and the franchise is anything more than understandable frustration with the state of the team.
Of course, Brady's frustrations could be linked to something deeper; he might be upset that the Patriots selected his eventual replacement in the 2nd round this year, effectively putting a timeline on his stay in New England. Perhaps he thought the team would take a quarterback later in the draft, to leave room for the franchise to draft his replacement when it was closer to his 40th birthday.
Perhaps he thought the Patriots could have used the 2nd round pick on a better option- a wide receiver, perhaps, or a tight end to complement Rob Gronkowski. Instead, the team opted to trade one of the offensive linemen in exchange for the complementary tight end.
But based on these reports, I wouldn't read anything more into it beyond Brady just being human. Anyone who wouldn't be frustrated with the situation is either not a competitor, or not human.
Also, note that Mort has stirred this pot once before, back in 2010, citing Brady's unhappiness being "above a 5, on a scale of 1 to 10" with regards to his new contract. Mort said that Brady was unhappy with the offers, the relationship was "chilled," and thought that Brady should receive a Peyton Manning-like contract for $20 million per season.
Of course, the Patriots paid Brady and gave him a contract that would make him (at the time) the highest paid quarterback from 2011 to 2014. The team went on to make three Conference Championships and one Super Bowl after the relationship "chilled," so maybe winning heals everything.