It seems like the image has a /usr/local/bin/autoconf installed, which doesn't recognize/work with the yum installed libtools. Putting distributed binaries/libraries first solves the problem
@@ -47,6 +47,9 @@ cd $DIR/protobuf-${PROTOBUF_VERSION}
sed -i '/AC_PROG_OBJC/d' configure.ac
sed -i 's/conformance\/Makefile//g' configure.ac
+# Use the /usr/bin/autoconf and related tools to pick the correct aclocal macros
+export PATH="/usr/bin:$PATH"
+
# Build protoc
./autogen.sh
CXXFLAGS="-fPIC -g -O2" ./configure