bin/flume should respect HADOOP_CONF_DIR and use core and hdfs settings from there.

If fs.default.name is to hdfs://localhost:8020 in /etc/hadoop/conf/core-site.xml this command line should echo

$ HADOOP_CONF_DIR=/etc/hadoop/conf bin/flume class com.cloudera.flume.conf.FlumeConfiguration | grep fs.default
<property><name>fs.default.name</name><value>hdfs://localhost:8020/</value></property>

Currently with the default configuration this outputs:
<property><name>fs.default.name</name><value>file:///</value></property>