I am not familiar with fluentd, so do not know if it provides some type of default mapping like Logstash does or not. Check if you have any index templates defined that would apply to the index these logs go into. If this is the case you should be able to modify the mapping for the timestamp field so that Elasticsearch maps it as a date.
If you do not have a template defined and rely on dynamic mapping, you can create an index template with a mapping and specify the date formats Elasticsearch uses to identify date fields.