I'm here to say, first of all, I'm neither saying Jones is bad nor am I saying Jones is good. He's still on my watch list.
There's a couple of points I have to bring up in light of what you presented. First, as much as fantasy stats don't tell an entire tale it was a well-established plus match-up most of last year to use your TE if they were playing Dallas. I believe the Dallas D was 32nd against TEs for a significant portion of the season. This is a bad thing if the team heralds Jones as being their TE stopper. Second, if we want to just toss the fantasy angle out the window and look at games where TEs had monster production it constitutes more than just the Chicago game***:
Playoffs Cook 103 yds, 1 TD Jones played 94% of snaps
Week 17 Ertz 139 yds, 2 TDs Jones played 89% of snaps
Week 16 Ebron 93 yds Jones played 100% of snaps
Week 15 Brate 73 yds, 1 TD Jones played 98% of snaps
Week 12 Reed 95 yds, 2 TDs Jones played 100% of snaps
Week 4 Celek 79 yds Jones played on 77% of snaps
Week 3 Miller - Already accounted for Jones played on 83% of snaps
Week 2 Reed 70 yds Jones played 99% of snaps - this is a good one for Jones but I think Reed might have still been hurt
Looking at this data I came away impressed by how much Jones does the most important thing a player can do: be out on the field and compete. He played a large portion of snaps. It's also key to note the snap percentage isn't the percentage of time he was on the TEs mentioned. He might have been on the other side of the field for all I know.
However, to place the blame for his poor passer-rating-against on one contest in Week 3 may be slightly disingenuous. There were other games where the TE was a plus match-up to the opponent and showed in the stats.
***Note: I didn't watch these games to know who did what on which play so for all I know Jones never covered any of these TEs in the game. But it would make sense for his passer-rating-against to be so bad if he was victimized several times for a TE's best game of the year or an obviously strong game from a TE.