She wanted to show the Capitol that they were responsible for the death of Rue and so many other children who hadn't gotten to live their lives. Katniss didn't want Panem to remember Rue like this. She covered her in flowers to really make it look like she was just sleeping in a meadow.
Rue was her friend she didn’t just want to leave her body there and she couldn’t bury her so she decided to cover her is flowers to show her respect and to let her rest
