I'm having the same problem with my Belkin Tunecast since upgrading to 4.3 and it's now worse with 4.3.1. I'm at the Apple store now having them look at the issue.
You're not the only one. Apparently the software upgrade doesn't agree. Apple says my phone is fine and could just be an incompatibility between Belkin and the new update. Hopefully it will be fixed in a future bug fix.
I've also had this issue with charging since upgrading to iOS 4.3.1 Actually upgrading to 4.3.2 and then to 4.3.3 has not solved the charging problem. Here's my story:
I own an iPhone 3GS and started noticing error messages with 4.3.1 such as "charging is not supported with this accessory". I've tried differnent USB cables and chargers (Apple and non-Apple), hooking up to computers and wall outlets. I get the same message. As a last resort I restored my device as a new phone (syncing works oddly) and erasing everything. This did not help the situation.
So yesterday I took my 3GS to the Apple Store and they were kind enough to replace my iPhone with a new (refurbished) 3GS under AppleCare. That was awesome - I love Apple. However, that didn't fix the problem
So now I'm not sure what to do accept wait for a new iOS version and hope Apple addresses this problem. Anyone else have a similar experience?