Parse Flags enum from array of booleans

Well, you need some sort of mapping between the parameters and the enum values, so you can't actually avoid having three almost same pieces of code. But you can make your code shorter by using ifs and |= instead of ternary operators:

private UserContactPreferences GetContactPreferences(bool email, bool phone, bool sms)
{
    var preferences = UserContactPreferences.None;

    if (email)
        preferences |= UserContactPreferences.Email;
    if (phone)
        preferences |= UserContactPreferences.Phone;
    if (sms)
        preferences |= UserContactPreferences.SMS;

    return preferences;
}

If you had more parameters (though that would be a code smell), it might be worth considering something like using a dictionary. But I'm not sure it's a good idea, it's certainly longer than the previous version:

private UserContactPreferences GetContactPreferences(bool email, bool phone, bool sms)
{
    var dictionary = new Dictionary<UserContactPreferences, bool>
    {
        { UserContactPreferences.Email, email },
        { UserContactPreferences.Phone, phone },
        { UserContactPreferences.SMS, sms }
    };

    var preferences = UserContactPreferences.None;

    foreach (var kvp in dictionary)
    {
        if (kvp.Value)
            preferences |= kvp.Key;
    }

    return preferences;
}