Note, on this tutorial we will be using iFile. Alternatively, you can navigate to Root/Applications/Cydia.app using iFunbox, or iExplorer. You can also SSH [Windows] [Mac]. Note that before you can use iFunbox or iExplorer on iOS 7 you must install afc2add from Cydia! Otherwise your device will not be seen! The evasi0n7 jailbreak for some reason did not include this package automatically.
Jailbreak your device. You can find instructions on how to do that here.
Launch Cydia from your Springboard.
Select the Sections tab.
Tap to choose System from the list of sections.
Select iFile from the list of packages.
Press the Install button at the top right hand corner of the screen.
Press Confirm to begin installation.
Tap the large Return to Cydia button once installation has completed.
Press the Home button and launch Safari from the SpringBoard.
Navigate to http://www.iclarified.com/files/cydia/cydia-icon.zip. This will download an unofficial icon created by iHaz3. You can find several other icon designs listed here. Reddit users D4RKL0RD198 and diegoisawesome provided zipped up packages as alternatives. An iClarified commenter also pointed us to this nice icon design as well (Thanks!)
Tap the Open in "iFile" button at the top right.
Once iFile opens the archive, tap the Unarchiver button. Then tap done when the extraction is complete.
Tap to open the Cydia Icon All Devices folder that was created.
Press the Edit button and select all the Icon files listed.
Tap the Clipboard icon at the bottom right and then choose Copy/Link. Tap Done.
Tap the back button at the top left until your reach root ('/'), then tap Applications, then Cydia.app.
Scroll down the "Icon" files and tap one. Rename it to end with ".bak" then tap Done. Repeat this for each of the files that begin with "Icon".
Once all the files have been renamed tap Edit. Then tap the Clipboard icon at the bottom right hand corner. Choose Paste from popup buttons. Then tap Done and restart your phone.
Once your phone reboots you will have a nice new Cydia icon!
***Thanks to iHaz3 for the new icon design!