How can i protect agains incomming hackers?

Dear Piwik,

The last few months I have hacking activity on my website. From defacing the homepage to fake DHL scrips.
If I look in the Securi plugin logs I see this.

juli 29, 2015 9:58 am system ::1 New file added: (multiple entries):

•.htaccess (size: 395483)
•0x3a.php (size: 2424)
•HenewjQJGUPo2yZtLk8Ab0aDko.html
•googleaa334dc267f88ef8.html
•indonesia.php

•php.ini
•piwik/bower.json
•piwik/composer.json
•piwik/config/.htaccess
•piwik/config/config.ini.php
•piwik/config/environment/cli.php
•piwik/config/environment/dev.php
•piwik/config/environment/test.php
•piwik/config/global.ini.php
•piwik/config/global.php
•piwik/config/manifest.inc.php
•piwik/core/.htaccess
•piwik/core/API/ApiRenderer.php
•piwik/core/API/CORSHandler.php
•piwik/core/API/DataTableGenericFilter.php
•piwik/core/API/DataTableManipulator.php
•piwik/core/API/DataTableManipulator/Flattener.php
•piwik/core/API/DataTableManipulator/LabelFilter.php
•piwik/core/API/DataTableManipulator/ReportTotalsCalculator.php
•piwik/core/API/DataTablePostProcessor.php
•piwik/core/API/DocumentationGenerator.php
•piwik/core/API/Inconsistencies.php
•piwik/core/API/Proxy.php
•piwik/core/API/Request.php
•piwik/core/API/ResponseBuilder.php
•piwik/core/Access.php
•piwik/core/Archive.php
•piwik/core/Archive/ArchiveInvalidator.php
•piwik/core/Archive/ArchivePurger.php
•piwik/core/Archive/Chunk.php
•piwik/core/Archive/DataCollection.php
•piwik/core/Archive/DataTableFactory.php
•piwik/core/Archive/Parameters.php
•piwik/core/ArchiveProcessor.php
•piwik/core/ArchiveProcessor/Loader.php
•piwik/core/ArchiveProcessor/Parameters.php
•piwik/core/ArchiveProcessor/PluginsArchiver.php
•piwik/core/ArchiveProcessor/Rules.php
•piwik/core/Archiver/Request.php
•piwik/core/AssetManager.php
•…

Does this mean Piwik is the weakest link in my secutiy or could the leak be anywhere? Maybe I did the installation not the right way?

Could you give me some tips how to protect myself against these attacks.