How to download multiple proteomes at once?
You could try download-refseq-genomes. It will fetch all genomes from the NCBI FTP server that are in a specific subtree of the phylogeny. 

For example, downloading the amino acid sequences from all proteins in each genome assembly for all species belonging to Chloroflexi (NCBI taxon ID = 200795):

download-refseq-genomes.pl -t faa 200795


This will download all assemblies with status=Complete. Use option -a to download all assemblies with any status.