Your Flag collection, as it gets higher, allows you to buy more advanced equipment at the Secret Base shop in Fortree City. At 30, you reach Bronze rank, Silver at 100, Gold at 500, and Platinum at 1,000. At each rank-up, you get a reward.
Secret Base Guild Rank Rewards:
Bronze Rank - 30 Flags - Blackboard
Silver Rank - 100 Flags - Jukebox
Gold Rank - 500 Flags - Mood Lighting
Platinum Rank - 1,000 Flags - Confetti and Garchompite
Note: You must talk to Aarune after you've collected enough flags to rank up, you do not rank up automatically.