I have a way to make it work, but there are 2 "gotchas" that I am not very pleased with. 
First, changing your xsd to this:
<xs:element name="Cart">
        <xs:complexType>
            <xs:all>
                <xs:element name="id" type="xs:string" minOccurs="0" maxOccurs="1" />
                <xs:element name="name" type="xs:string" minOccurs="0" maxOccurs="1" />
                <xs:element name="owner_id" type="xs:string" minOccurs="0" maxOccurs="1" />
                <xs:element  name="ownerEmail" type="xs:string" minOccurs="0" maxOccurs="1" />
            </xs:all>
        </xs:complexType>
    </xs:element>
And then you can create bindings file to generate the transient annotation as mentioned to you by other users:
<jxb:bindings
        xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
        xmlns:xs="http://www.w3.org/2001/XMLSchema"
        xmlns:xjc="http://java.sun.com/xml/ns/jaxb/xjc"
        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
        xmlns:annox="http://annox.dev.java.net"
        xsi:schemaLocation="http://java.sun.com/xml/ns/jaxb http://java.sun.com/xml/ns/jaxb/bindingschema_2_0.xsd"
        jxb:extensionBindingPrefixes="xjc annox" version="2.1">
    <jxb:bindings schemaLocation="../xsd/cart.xsd">
        <jxb:bindings node="//xs:element[@name='Cart']//xs:complexType//xs:all//xs:element[@name='ownerEmail']">
            <annox:annotate target="field">
                <annox:annotate annox:class="javax.xml.bind.annotation.XmlTransient" />
            </annox:annotate>
        </jxb:bindings>
    </jxb:bindings>
</jxb:bindings>
This would generate when marshaling the following xml:
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<Cart>
    <id>id</id>
    <name>name</name>
    <owner_id>owner id</owner_id>
</Cart>
The gotchas:
- The sequence of elements became xs:all, if not it would create a
propOrder in the POJO and this would also list the transient field
and would cause problems
- Renamed field "owner_email" to "ownerEmail" because the first version
would generate (along with transient) @XmlElement with the
owner_email name and have the field according to naming conventions. - I will try to see if I can find workaround for these but for now maybe this helps. Cheers!