Coveo.IsPublishableInboundFilter.config

<configuration xmlns:patch="http://www.sitecore.net/xmlconfig/">
  <sitecore>
    <pipelines>
      <coveoInboundFilterPipeline>
        <processor type="MySolution.Coveo.Custom.InboundFilters.IsPublishableInboundFilter, MySolution.Coveo.Custom" />
      </coveoInboundFilterPipeline>
    </pipelines>
  </sitecore>
</configuration>

IsPublishableInboundFilter.cs

using Coveo.Framework.Items;
using Coveo.SearchProvider.InboundFilters;
using Coveo.SearchProvider.Pipelines;

namespace MySolution.Coveo.Custom.InboundFilters
{
    public class IsPublishableInboundFilter : AbstractCoveoInboundFilterProcessor
    {
        public override void Process(CoveoInboundFilterPipelineArgs args)
        {
            if (args.IndexableToIndex != null && !args.IsExcluded && ShouldExecute(args))
            {
                var item = args.IndexableToIndex.Item;

                if (item.Publishing.NeverPublish)
                {
                    args.IsExcluded = true;
                    return;
                }

                args.IsExcluded = !AllAncestorsArePublishable(item);
            }
        }

        private bool AllAncestorsArePublishable(IItem item)
        {
            if (item.Parent != null && item.Parent.Publishing.NeverPublish)
            {
                return false;
            }
            else if (item.Parent != null)
            {
                return AllAncestorsArePublishable(item.Parent);
            }

            return true;
        }
    }
}

Updated based on feedback from @jflheureux from Coveo. Thank you, Jeff!