User, tell us your exact JDev version, please!
The width of the fields in an af:query depends on the width of the attribute behind it. You can change the display width of these attributes. If this doesn't work it'll be very hard to archive as you can't easily change the look and feel of the af:query component.
JDev Ver - 220.127.116.11
Your af:query, I suppose, is based on View Criteria. Go to the View Object that defines the View Criteria --> Go to View Criteria tab --> Select the View Criteria that your af:query is based on --> Click on Edit (pencil) icon.
In the Edit View Criteria popup --> In Criteria Definition Tab --> Select attributes that map to Text fields in your search page, one at a time, that you want to resize --> in the same Criteria Definition tab, select Item Ui Hints tab --> Specify a Value for Width (in Characters).
What I noticed is drop downs don't honor the width, however, text fields do. Therefore, your best best would be to resize the text fields to match the size of the drop downs. Setting the Width at View Criteria level rather than View Object level will limit the impact of this change to only the search page. However, if you do want to enforce the same width across all pages where the View Object is used then you can specify the width at View Object attribute level as well.