I doubt you could do it that way, unless possibly you gave all the indigogo money directly to the charity - even then it might be pretty difficult.
What you can do is find a non-profit organization to be your 'fiscal sponsor'. What this set up donations go directly to them - so they are tax deductible - and then they give the funds to you as part of their normal operations. Generally they will keep a portion of the money donated, 5-10%, although under some agreements that doesn't kick in until you hit a minimum level. It all depends on the agreement you work out with them, and many organizations that do this will have a standard agreement.
Under this model though they are essentially funding your project, even though the money may come to them from a variety of donors, grants, etc. This means for them to get involved your film will generally have to fit into whatever the mission of their organization is pretty directly. So a non-profit organization working to fight homelessness may be willing to be a fiscal sponsor on a film that has the plight of the homeless as it's central theme, but isn't likely to be interested in a romantic comedy or action film. Because of that it's more common for these relationships to happen with documentary films rather than fiction.
And even if you get a fiscal sponsor I don't know if you could raise the money through indigogo. The only way I could see it working is if the non-profit ran the campaign themselves, so that the money was going to them - but since the money goes to indigogo first, then is passed to the charity, I'm not sure how that works; you'd need to look into if indigogo has procedures in place for working with non-profits.