I tried with a sample project:
D:\dotnetDummy>dotnet publish
Microsoft (R) Build Engine version 15.3.409.57025 for .NET Core
Copyright (C) Microsoft Corporation. All rights reserved.
dotnetDummy -> D:\dotnetDummy\bin\Debug\netcoreapp2.0\dotnetDummy.dll
dotnetDummy -> D:\dotnetDummy\bin\Debug\netcoreapp2.0\publish\ <-- output directory
after publishing locally, you want to move all files under output directory to wwwroot folder of your azure webapp, in this case your D:\home\site\wwwroot on Kudu site should look the same as D:\dotnetDummy\bin\Debug\netcoreapp2.0\publish
D:\dotnetDummy\bin\Debug\netcoreapp2.0\publish>dir /B
dotnetDummy.deps.json
dotnetDummy.dll
dotnetDummy.pdb
dotnetDummy.PrecompiledViews.dll
dotnetDummy.PrecompiledViews.pdb
dotnetDummy.runtimeconfig.json
web.config <-- output of dotnet publish
if you don't see web.config under wwwroot, I would guess there's a mistake during the move