Which OS are you using?
If you are on Windows you might need to use Zadig to select a different USB driver.
To begin, download Zadig. Use the most recent version.
Launch Zadig and then put the Daisy into bootloader mode by holding BOOT and pressing RESET.
Click the Options menu in Zadig and select “List All Devices.”
In the drop down menu inside the main window, select “DFU in FS mode,” followed by selecting WinUSB in the target driver box.
Click “Replace Driver.” Zadig will update to the appropriate driver to flash Daisy.
These instructions are also in the Windows Toolchain Install Wiki page on GitHub with screenshots.
edit: To clarify, Zadig is not only for command line programming but can be used for the Web Progammer as well on Windows. It should fix the connectivity problem if the USB driver is to blame.