Fact is, sometimes when the President is doing the best things is when he has especially low ratings.
For example, we all think (except a few radical Libertarians) the civil rights bills were a good thing eliminating segregation and helping voter rights etc.
But JFK had to delay the bills because they threatened his entire agenda, and LBJ recognized he was 'handing the White House to Republicans' by passing them.
A rare exception is that when FDR had his first term, ratings were pretty high for his battle against the Great Depression.