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I can't think of a good reason to run Alfresco as root. I can think of a lot of good reasons not to.
To check, just do ps -ef|grep alfresco and look to see who owns the process. Here's an example:
ubuntu@some-host:~$ ps -ef|grep tomcat ubuntu 943 922 0 18:24 pts/0 00:00:00 grep --color=auto tomcat alfresco 25682 1 28 Sep02 ? 5-14:28:30 /opt/alfresco/java/bin/java -Djava.util.logging.config.file=/opt/alfresco/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512M -Xmx3992M -XX:+DisableExplicitGC -XX:+UseConcMarkSweepGC -XX:+UseParNewGC -Djava.awt.headless=true -Dalfresco.home=/opt/alfresco -XX:ReservedCodeCacheSize=128m -Xmx2G -Djavax.net.ssl.keyStore=/data/alf_data/keystore/someKeystore.jks -Djavax.net.ssl.keyStorePassword=ue27Uc5ZiFwV -Djava.endorsed.dirs=/opt/alfresco/tomcat/endorsed -classpath /opt/alfresco/tomcat/bin/bootstrap.jar:/opt/alfresco/tomcat/bin/tomca-juli.jar -Dcatalina.base=/opt/alfresco/tomcat -Dcatalina.home=/opt/alfresco/tomcat -Djava.io.tmpdir=/opt/alfresco/tomcat/temp org.apache.catalina.startup.Bootstrap start
That "alfresco" next to 25682 says this process is running as the alfresco user, not root, which is what you want.