This is ticky-tacky enforcement. The players had already agreed to new contracts through their agents, and the infraction is the Falcons talking directly to the players to arrange travel AFTER the contracts were already agreed upon. I'm not saying that the NFL should let the Falcons off the hook. But the relatively low penalty of a 5th round pick reflects the relatively minor nature of the infraction. I'm not sure what Terry Fontenot makes as a salary, but assuming he makes at least $5M per season, a $50K fine for him is the equivalent of a $650 fine for someone who makes $65K per year. And the $250K fine for the Falcons is a slap on the wrist.
Based on the available information, a slap on the wrist was an appropriate penalty for a first offense.