In my opinion, he has deserved better. He's the most over babyface on the roster, nobody else even comes close at this point, not Cena, not Ambrose, not Orton and certainly not Reigns. Fans WANT to cheer for him and genuinely LIKE cheering for him, they like hearing him talk and they like watching him inside the ring. He sells a lot of merchandise and his segments are often among the top drawing segments, often THE top drawing segment, on WWE TV. He draws and helps bring a lot of money for the company, that should be THE primary concern WWE has in regards to any wrestler on the roster.
However, I'm not going to completely rake WWE over the coals because MAYBE there's concern over Bryan's condition in the long run. Bryan just returned to action at the Royal Rumble and was cleared only a few weeks prior to the Rumble. While Bryan was cleared to wrestle, his neck issue is something that obviously raised concerns and rightly so. Bryan's only been back in action for about 2.5 months and his return happened to come about during WrestleMania season. MAYBE WWE officials were reluctant to put Bryan in the main event with Lesnar at the biggest show of the year because they had no real way of knowing how Bryan's neck would hold up. A match with Lesnar would be extremely physical, so without any real knowledge as to how he'd hold up, MAYBE they didn't want to risk it. The only way to know Bryan's neck will hold up in the long run is with the passage of time and if they felt that enough time hadn't passed for them to gauge how Bryan would do, then I can at least understand that. I'm not saying that's the case, but it makes a lot more sense than pushing Reigns mostly because Vince likes how he looks.
If Daniel Bryan wins the Intercontinental Championship, it could be the beginning of Bryan's journey back to the main event picture. IF Bryan is booked as a strong & relevant champion in a long & significant run as champion giving officials enough time to see how his neck is holding up, it MIGHT be the launching pad for Bryan to get back to the WWE World Heavyweight Championship a bit later down the line.