This change skips ECDSA signature verification for transactions during the initial block-chain download, which makes downloading the block chain much faster.
"Initial block chain download" is all blocks up to 120 blocks before the last blockchain lock-in point.
Reasoning for why this is safe:
If an attacker tries to feed a client bad transactions during the initial block-chain download (transactions with invalid signatures), then they change the merkle tree, and at the first blockchain lock-in the bad chain will be rejected.
Transactions are still checked for orphan blocks that come in during initial block-chain-download (ConnectInputs will be called with fBlock=FALSE) and for mined blocks (ConnectInputs called with fMiner=TRUE).